RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

210 rows where devstage_curation_coarse = "Embryo" and tissue_curation = "Multi-tissue"

✎ View and edit SQL

This data as json, CSV (advanced)

technology 5

devstage_curation 5

experiment.library_selection 3

experiment.platform 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 210 ✖

experiment.library_strategy 1

devstage_curation_coarse 1

  • Embryo · 210 ✖
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
175 175 DRR084197 DRX078028 DRS086522 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     natural paring early sample zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2] SAMD00073604   sample name:M 4th|replicate:biological replicate 2                 Illumina HiSeq 2500 sequencing of SAMD00073604 DRX078028 zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073604       1389837888.0 38606608.0 DRR084197 0:36 A:320671418;C:336948866;G:347550258;T:381720581;N:2946765 36       320671418 336948866 347550258 381720581 2946765 DRX078028 DRS086522 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.89763   0.02235   0.76445   0.46381   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Zygote Embryo Multi-tissue Multi-system
181 181 DRR084191 DRX078022 DRS086516 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     natural paring early sample zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1] SAMD00073598   sample name:M|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073598 DRX078022 zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073598       1050981012.0 29193917.0 DRR084191 0:36 A:241048832;C:256186268;G:260277071;T:293299597;N:169244 36       241048832 256186268 260277071 293299597 169244 DRX078022 DRS086516 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.9088   0.02369   0.7624   0.47998   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Zygote Embryo Multi-tissue Multi-system
10188 10188 ERR600685 ERX557514 ERS460539 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537630 SC ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:42:28Z|External Id:SAMEA2537630|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:42:28Z|INSDC status:public|Submitter Id:stI oocytes TC9 WT F sc 1951842|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TCGAAGTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC9 WT F sc 1951842|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#9 10325318 Illumina sequencing of library 10325318 constructed from sample accession ERS460539 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TCGAAGTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#9.cram cram 2109545984.0 16480828.0 SC RUN 13129 8#9 0:53 1:75 A:539694535;C:346663352;G:388843341;T:829045236;N:5299520 53 75     539694535 346663352 388843341 829045236 5299520 ERX557514 ERS460539 ERA358077 SC Wellcome Sanger Institute 2 0.39712 0.80906 0.2298 0.0288 0.97575 0.82292 0.20258 0.50014 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10189 10189 ERR600684 ERX557513 ERS460538 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537629 SC ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537629|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC8 buc 4 sc 1951841|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TTCCATTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC8 buc 4 sc 1951841|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#8 10325317 Illumina sequencing of library 10325317 constructed from sample accession ERS460538 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TTCCATTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#8.cram cram 1995224064.0 15587688.0 SC RUN 13129 8#8 0:53 1:75 A:508909383;C:332355977;G:373835062;T:775089830;N:5033812 53 75     508909383 332355977 373835062 775089830 5033812 ERX557513 ERS460538 ERA358077 SC Wellcome Sanger Institute 2 0.31242 0.8426 0.16835 0.02824 0.96921 0.81606 0.27677 0.49882 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10190 10190 ERR600683 ERX557512 ERS460537 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537628 SC ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:57:23Z|External Id:SAMEA2537628|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:57:23Z|INSDC status:public|Submitter Id:stI oocytes TC7 buc 3 sc 1951840|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TAGTCTTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC7 buc 3 sc 1951840|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#7 10325316 Illumina sequencing of library 10325316 constructed from sample accession ERS460537 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TAGTCTTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#7.cram cram 1335316864.0 10432163.0 SC RUN 13129 8#7 0:53 1:75 A:318582120;C:238156133;G:258642941;T:516548945;N:3386725 53 75     318582120 238156133 258642941 516548945 3386725 ERX557512 ERS460537 ERA358077 SC Wellcome Sanger Institute 2 0.32517 0.89235 0.16229 0.04485 0.97634 0.90057 0.32073 0.47925 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10191 10191 ERR600682 ERX557511 ERS460536 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537627 SC ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:42:28Z|External Id:SAMEA2537627|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:42:28Z|INSDC status:public|Submitter Id:stI oocytes TC6 buc 2 sc 1951839|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TGTGGTTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC6 buc 2 sc 1951839|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#6 10325315 Illumina sequencing of library 10325315 constructed from sample accession ERS460536 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TGTGGTTG. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#6.cram cram 2044001792.0 15968764.0 SC RUN 13129 8#6 0:53 1:75 A:525134102;C:334554692;G:372135205;T:806953076;N:5224717 53 75     525134102 334554692 372135205 806953076 5224717 ERX557511 ERS460536 ERA358077 SC Wellcome Sanger Institute 2 0.32466 0.83888 0.17696 0.03057 0.97451 0.82938 0.2392 0.48605 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10192 10192 ERR600681 ERX557510 ERS460535 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537626 SC ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537626|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC5 buc 1 sc 1951838|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TCCTCAATAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC5 buc 1 sc 1951838|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#5 10325314 Illumina sequencing of library 10325314 constructed from sample accession ERS460535 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TCCTCAAT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#5.cram cram 2936817024.0 22943883.0 SC RUN 13129 8#5 0:53 1:75 A:708314449;C:473731341;G:531306146;T:1215982569;N:7482519 53 75     708314449 473731341 531306146 1215982569 7482519 ERX557510 ERS460535 ERA358077 SC Wellcome Sanger Institute 2 0.38759 0.88578 0.22255 0.03034 0.9707 0.80984 0.2075 0.47267 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10193 10193 ERR600680 ERX557509 ERS460534 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537625 SC ArrayExpress Genotype:Tgbuc:del80|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:57:23Z|External Id:SAMEA2537625|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:57:23Z|INSDC status:public|Submitter Id:stI oocytes TC4 Tg 1 sc 1951837|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TACAGGATAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC4 Tg 1 sc 1951837|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#4 10325313 Illumina sequencing of library 10325313 constructed from sample accession ERS460534 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TACAGGAT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#4.cram cram 2384869248.0 18631791.0 SC RUN 13129 8#4 0:53 1:75 A:579389373;C:378753292;G:429075103;T:991563565;N:6087915 53 75     579389373 378753292 429075103 991563565 6087915 ERX557509 ERS460534 ERA358077 SC Wellcome Sanger Institute 2 0.48038 0.84929 0.28951 0.03671 0.97788 0.81249 0.13153 0.4899 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10194 10194 ERR600679 ERX557508 ERS460533 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537624 SC ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:42:28Z|External Id:SAMEA2537624|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:42:28Z|INSDC status:public|Submitter Id:stI oocytes TC3 WT 3 sc 1951836|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TAGTGACTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC3 WT 3 sc 1951836|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#3 10325312 Illumina sequencing of library 10325312 constructed from sample accession ERS460533 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TAGTGACT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#3.cram cram 2105031424.0 16445558.0 SC RUN 13129 8#3 0:53 1:75 A:508334707;C:332423893;G:374815782;T:884154321;N:5302721 53 75     508334707 332423893 374815782 884154321 5302721 ERX557508 ERS460533 ERA358077 SC Wellcome Sanger Institute 2 0.50684 0.84751 0.30664 0.04222 0.97853 0.81343 0.11336 0.49639 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10195 10195 ERR600678 ERX557507 ERS460532 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537623 SC ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537623|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC2 WT 2 sc 1951835|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TTCCTGCTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC2 WT 2 sc 1951835|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#2 10325311 Illumina sequencing of library 10325311 constructed from sample accession ERS460532 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TTCCTGCT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#2.cram cram 1616469504.0 12628668.0 SC RUN 13129 8#2 0:53 1:75 A:415492342;C:254209235;G:288719848;T:653979238;N:4068841 53 75     415492342 254209235 288719848 653979238 4068841 ERX557507 ERS460532 ERA358077 SC Wellcome Sanger Institute 2 0.44661 0.81908 0.25181 0.0449 0.96469 0.80306 0.22578 0.49499 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10196 10196 ERR600677 ERX557506 ERS460531 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2537622 SC ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:57:22Z|External Id:SAMEA2537622|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:57:22Z|INSDC status:public|Submitter Id:stI oocytes TC1 WT 1 sc 1951834|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TGCGATCTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC1 WT 1 sc 1951834|scientific name:Danio rerio|strain:AB                 Illumina HiSeq 2000 paired end sequencing SC EXP 13129 8#1 10325310 Illumina sequencing of library 10325310 constructed from sample accession ERS460531 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13129 8. This submission includes reads tagged with the sequence TGCGATCT. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003932 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16 13129_8#1.cram cram 1741512832.0 13605569.0 SC RUN 13129 8#1 0:53 1:75 A:460247357;C:265029516;G:295203994;T:716636989;N:4394976 53 75     460247357 265029516 295203994 716636989 4394976 ERX557506 ERS460531 ERA358077 SC Wellcome Sanger Institute 2 0.36591 0.79177 0.21838 0.03785 0.97569 0.81095 0.16098 0.49496 53 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-16 Zygote Embryo Multi-tissue Multi-system
10197 10197 ERR596433 ERX553396 ERS462797 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547987 SC ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547987|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction9 WT F sc 1971686|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction9 WT F sc 1971686|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#9 10347698 Illumina sequencing of library 10347698 constructed from sample accession ERS462797 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence GATCAG. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#9.cram cram 552103200.0 1840344.0 SC RUN 13147 1#9 0:150 1:150 A:124691243;C:154385942;G:155440122;T:117585893;N:0 150 150     124691243 154385942 155440122 117585893 0 ERX553396 ERS462797 ERA356861 SC Wellcome Sanger Institute 2 0.97349 0.97184 0.25562 0.26367 0.73754 0.76534 0.68526 0.65497 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
10198 10198 ERR596432 ERX553395 ERS462796 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547986 SC ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:35Z|External Id:SAMEA2547986|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:35Z|INSDC status:public|Submitter Id:stI oocytes Fraction8 buc 4 sc 1971685|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction8 buc 4 sc 1971685|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#8 10347697 Illumina sequencing of library 10347697 constructed from sample accession ERS462796 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence ACTTGA. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#8.cram cram 625194300.0 2083981.0 SC RUN 13147 1#8 0:150 1:150 A:145587865;C:170554648;G:171453968;T:137597813;N:6 150 150     145587865 170554648 171453968 137597813 6 ERX553395 ERS462796 ERA356861 SC Wellcome Sanger Institute 2 0.97066 0.96788 0.23219 0.23823 0.7205 0.75623 0.61734 0.60233 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
10199 10199 ERR596431 ERX553394 ERS462795 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547985 SC ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547985|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction7 buc 3 sc 1971684|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction7 buc 3 sc 1971684|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#7 10347696 Illumina sequencing of library 10347696 constructed from sample accession ERS462795 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence CAGATC. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#7.cram cram 498083400.0 1660278.0 SC RUN 13147 1#7 0:150 1:150 A:127449944;C:127409242;G:133869886;T:109354327;N:1 150 150     127449944 127409242 133869886 109354327 1 ERX553394 ERS462795 ERA356861 SC Wellcome Sanger Institute 2 0.94952 0.95502 0.14913 0.14846 0.73807 0.74572 0.54621 0.54335 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
10200 10200 ERR596430 ERX553393 ERS462794 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547984 SC ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547984|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction6 buc 2 sc 1971683|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction6 buc 2 sc 1971683|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#6 10347695 Illumina sequencing of library 10347695 constructed from sample accession ERS462794 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence GCCAAT. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#6.cram cram 433626600.0 1445422.0 SC RUN 13147 1#6 0:150 1:150 A:113030099;C:110060861;G:116695113;T:93840526;N:1 150 150     113030099 110060861 116695113 93840526 1 ERX553393 ERS462794 ERA356861 SC Wellcome Sanger Institute 2 0.94512 0.95418 0.13754 0.13509 0.76274 0.77542 0.54752 0.54127 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
10201 10201 ERR596429 ERX553392 ERS462793 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547983 SC ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:34Z|External Id:SAMEA2547983|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:34Z|INSDC status:public|Submitter Id:stI oocytes Fraction5 buc 1 sc 1971682|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction5 buc 1 sc 1971682|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#5 10347694 Illumina sequencing of library 10347694 constructed from sample accession ERS462793 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence ACAGTG. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#5.cram cram 670533600.0 2235112.0 SC RUN 13147 1#5 0:150 1:150 A:152057213;C:184952145;G:191337018;T:142187224;N:0 150 150     152057213 184952145 191337018 142187224 0 ERX553392 ERS462793 ERA356861 SC Wellcome Sanger Institute 2 0.95987 0.95954 0.20495 0.20606 0.73726 0.7529 0.61328 0.61986 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
10202 10202 ERR596428 ERX553391 ERS462792 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547982 SC ArrayExpress Genotype:Tgbuc:del80|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547982|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction4 Tg 1 sc 1971681|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction4 Tg 1 sc 1971681|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#4 10347693 Illumina sequencing of library 10347693 constructed from sample accession ERS462792 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence TGACCA. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#4.cram cram 524202300.0 1747341.0 SC RUN 13147 1#4 0:150 1:150 A:117529161;C:147865152;G:153007969;T:105800018;N:0 150 150     117529161 147865152 153007969 105800018 0 ERX553391 ERS462792 ERA356861 SC Wellcome Sanger Institute 2 0.95955 0.96175 0.21001 0.20834 0.76445 0.78281 0.70435 0.68975 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
10203 10203 ERR596427 ERX553390 ERS462791 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547981 SC ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547981|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction3 WT 3 sc 1971680|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction3 WT 3 sc 1971680|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#3 10347692 Illumina sequencing of library 10347692 constructed from sample accession ERS462791 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence TTAGGC. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#3.cram cram 1142124300.0 3807081.0 SC RUN 13147 1#3 0:150 1:150 A:239327535;C:334933829;G:339423780;T:228439155;N:1 150 150     239327535 334933829 339423780 228439155 1 ERX553390 ERS462791 ERA356861 SC Wellcome Sanger Institute 2 0.98041 0.98099 0.28225 0.28585 0.80273 0.81012 0.81256 0.81436 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
10204 10204 ERR596426 ERX553389 ERS462790 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547980 SC ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:34Z|External Id:SAMEA2547980|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:34Z|INSDC status:public|Submitter Id:stI oocytes Fraction2 WT 2 sc 1971679|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction2 WT 2 sc 1971679|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#2 10347691 Illumina sequencing of library 10347691 constructed from sample accession ERS462790 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence CGATGT. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#2.cram cram 714969600.0 2383232.0 SC RUN 13147 1#2 0:150 1:150 A:151578902;C:207835645;G:217545196;T:138009856;N:1 150 150     151578902 207835645 217545196 138009856 1 ERX553389 ERS462790 ERA356861 SC Wellcome Sanger Institute 2 0.97925 0.981 0.2548 0.25496 0.77447 0.78462 0.77035 0.76498 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
10205 10205 ERR596425 ERX553388 ERS462789 ERP003932 PRJEB4632 Zebrafish oocyte maturation Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777 Transcriptome Analysis The data within this study has been generated to study zebrafish oocyte maturation.         SAMEA2547979 SC ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547979|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction1 WT 1 sc 1971678|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction1 WT 1 sc 1971678|scientific name:Danio rerio|strain:AB                 Illumina MiSeq paired end sequencing SC EXP 13147 1#1 10347690 Illumina sequencing of library 10347690 constructed from sample accession ERS462789 for study accession ERP003932. This is part of an Illumina multiplexed sequencing run 13147 1. This submission includes reads tagged with the sequence ATCACG. RNA seq dUTP   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina MiSeq   ERP003932 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16 13147_1#1.cram cram 567682800.0 1892276.0 SC RUN 13147 1#1 0:150 1:150 A:133087363;C:153887726;G:158264603;T:122443107;N:1 150 150     133087363 153887726 158264603 122443107 1 ERX553388 ERS462789 ERA356861 SC Wellcome Sanger Institute 2 0.94832 0.94927 0.19305 0.19445 0.72421 0.73551 0.59172 0.60783 150 150 B B biological fallback assumption illumina miseq unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2014-09-09 Zygote Embryo Multi-tissue Multi-system
25091 25091 SRR25567703 SRX21296461 SRS18545739 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 Homo replicate 2 RNAseq GSM7696246   source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 Homo replicate 2 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. homozygous tie1 mutant embryos   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696246 GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq GSM7696246 r1 GSM7696246 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     413-Tie1-KO2_S4_L001_R1_001.fastq.gz fastq 445428400.0 5860900.0 GSM7696246 r1 0:76 A:143568074;C:79903177;G:79677344;T:142230186;N:49619 76       143568074 79903177 79677344 142230186 49619 SRX21296461 SRS18545739 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.75644   0.67481   0.78062   0.49002   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25092 25092 SRR25567704 SRX21296461 SRS18545739 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 Homo replicate 2 RNAseq GSM7696246   source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 Homo replicate 2 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. homozygous tie1 mutant embryos   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696246 GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq GSM7696246 r1 GSM7696246 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     413-Tie1-KO2_S4_L002_R1_001.fastq.gz fastq 436280280.0 5740530.0 GSM7696246 r2 0:76 A:140668025;C:78248456;G:77919880;T:139381210;N:62709 76       140668025 78248456 77919880 139381210 62709 SRX21296461 SRS18545739 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.75737   0.67543   0.77796   0.494   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25093 25093 SRR25567705 SRX21296461 SRS18545739 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 Homo replicate 2 RNAseq GSM7696246   source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 Homo replicate 2 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. homozygous tie1 mutant embryos   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696246 GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq GSM7696246 r1 GSM7696246 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     413-Tie1-KO2_S4_L003_R1_001.fastq.gz fastq 453115800.0 5962050.0 GSM7696246 r3 0:76 A:145977328;C:81331359;G:81042932;T:144726596;N:37585 76       145977328 81331359 81042932 144726596 37585 SRX21296461 SRS18545739 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.75941   0.67812   0.78255   0.49198   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25094 25094 SRR25567706 SRX21296461 SRS18545739 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 Homo replicate 2 RNAseq GSM7696246   source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 Homo replicate 2 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. homozygous tie1 mutant embryos   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696246 GSM7696246: EC tie1 Homo replicate 2 RNAseq; Danio rerio; RNA Seq GSM7696246 r1 GSM7696246 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     413-Tie1-KO2_S4_L004_R1_001.fastq.gz fastq 451629316.0 5942491.0 GSM7696246 r4 0:76 A:145539227;C:81081378;G:80692220;T:144283694;N:32797 76       145539227 81081378 80692220 144283694 32797 SRX21296461 SRS18545739 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.75907   0.67763   0.78074   0.49757   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25095 25095 SRR25567707 SRX21296460 SRS18545738 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 Homo replicate 1 RNAseq GSM7696245   source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 Homo replicate 1 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. homozygous tie1 mutant embryos   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696245 GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq GSM7696245 r1 GSM7696245 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     412-Tie1-KO1_S3_L001_R1_001.fastq.gz fastq 438903344.0 5775044.0 GSM7696245 r1 0:76 A:141636851;C:79318996;G:78779375;T:139120411;N:47711 76       141636851 79318996 78779375 139120411 47711 SRX21296460 SRS18545738 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.76357   0.65866   0.76238   0.48958   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25096 25096 SRR25567708 SRX21296460 SRS18545738 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 Homo replicate 1 RNAseq GSM7696245   source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 Homo replicate 1 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. homozygous tie1 mutant embryos   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696245 GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq GSM7696245 r1 GSM7696245 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     412-Tie1-KO1_S3_L002_R1_001.fastq.gz fastq 429344216.0 5649266.0 GSM7696245 r2 0:76 A:138620131;C:77579442;G:76950101;T:136131396;N:63146 76       138620131 77579442 76950101 136131396 63146 SRX21296460 SRS18545738 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.76216   0.65728   0.76132   0.4958   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25097 25097 SRR25567709 SRX21296460 SRS18545738 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 Homo replicate 1 RNAseq GSM7696245   source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 Homo replicate 1 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. homozygous tie1 mutant embryos   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696245 GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq GSM7696245 r1 GSM7696245 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     412-Tie1-KO1_S3_L003_R1_001.fastq.gz fastq 446301792.0 5872392.0 GSM7696245 r3 0:76 A:143941333;C:80689335;G:80111561;T:141523625;N:35938 76       143941333 80689335 80111561 141523625 35938 SRX21296460 SRS18545738 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.76416   0.65858   0.76177   0.48634   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25098 25098 SRR25567710 SRX21296460 SRS18545738 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 Homo replicate 1 RNAseq GSM7696245   source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 Homo replicate 1 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. homozygous tie1 mutant embryos   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696245 GSM7696245: EC tie1 Homo replicate 1 RNAseq; Danio rerio; RNA Seq GSM7696245 r1 GSM7696245 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     412-Tie1-KO1_S3_L004_R1_001.fastq.gz fastq 443971252.0 5841727.0 GSM7696245 r4 0:76 A:143197029;C:80287228;G:79639533;T:140816381;N:31081 76       143197029 80287228 79639533 140816381 31081 SRX21296460 SRS18545738 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.77093   0.66467   0.76081   0.49407   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25099 25099 SRR25567711 SRX21296459 SRS18545737 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 WT/Het replicate 2 RNAseq GSM7696244   source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 WT/Het replicate 2 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. wild type and heterozygous siblings   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696244 GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq GSM7696244 r1 GSM7696244 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     411-Tie1-WT-HT2_S2_L001_R1_001.fastq.gz fastq 392537796.0 5164971.0 GSM7696244 r1 0:76 A:124144181;C:72762157;G:72562894;T:123025322;N:43242 76       124144181 72762157 72562894 123025322 43242 SRX21296459 SRS18545737 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.78106   0.59772   0.73553   0.48949   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25100 25100 SRR25567712 SRX21296459 SRS18545737 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 WT/Het replicate 2 RNAseq GSM7696244   source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 WT/Het replicate 2 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. wild type and heterozygous siblings   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696244 GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq GSM7696244 r1 GSM7696244 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     411-Tie1-WT-HT2_S2_L002_R1_001.fastq.gz fastq 384487572.0 5059047.0 GSM7696244 r2 0:76 A:121620414;C:71266999;G:70967086;T:120577709;N:55364 76       121620414 71266999 70967086 120577709 55364 SRX21296459 SRS18545737 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.77986   0.59517   0.73547   0.48651   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25101 25101 SRR25567713 SRX21296459 SRS18545737 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 WT/Het replicate 2 RNAseq GSM7696244   source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 WT/Het replicate 2 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. wild type and heterozygous siblings   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696244 GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq GSM7696244 r1 GSM7696244 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     411-Tie1-WT-HT2_S2_L003_R1_001.fastq.gz fastq 399939360.0 5262360.0 GSM7696244 r3 0:76 A:126400057;C:74196301;G:73931308;T:125379595;N:32099 76       126400057 74196301 73931308 125379595 32099 SRX21296459 SRS18545737 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.77917   0.59465   0.7359   0.48952   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25102 25102 SRR25567714 SRX21296459 SRS18545737 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 WT/Het replicate 2 RNAseq GSM7696244   source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 WT/Het replicate 2 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. wild type and heterozygous siblings   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696244 GSM7696244: EC tie1 WT/Het replicate 2 RNAseq; Danio rerio; RNA Seq GSM7696244 r1 GSM7696244 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     411-Tie1-WT-HT2_S2_L004_R1_001.fastq.gz fastq 398035712.0 5237312.0 GSM7696244 r4 0:76 A:125843687;C:73845902;G:73489490;T:124828195;N:28438 76       125843687 73845902 73489490 124828195 28438 SRX21296459 SRS18545737 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.77934   0.59613   0.73608   0.48475   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25103 25103 SRR25567715 SRX21296458 SRS18545736 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 WT/Het replicate 1 RNAseq GSM7696243   source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 WT/Het replicate 1 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. wild type and heterozygous siblings   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696243 GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq GSM7696243 r1 GSM7696243 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     410-Tie1-WT-HT1_S1_L001_R1_001.fastq.gz fastq 412291944.0 5424894.0 GSM7696243 r1 0:76 A:129182868;C:77123147;G:77053023;T:128887593;N:45313 76       129182868 77123147 77053023 128887593 45313 SRX21296458 SRS18545736 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.79085   0.52962   0.7349   0.48594   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25104 25104 SRR25567716 SRX21296458 SRS18545736 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 WT/Het replicate 1 RNAseq GSM7696243   source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 WT/Het replicate 1 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. wild type and heterozygous siblings   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696243 GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq GSM7696243 r1 GSM7696243 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     410-Tie1-WT-HT1_S1_L002_R1_001.fastq.gz fastq 404294768.0 5319668.0 GSM7696243 r2 0:76 A:126685179;C:75658897;G:75455501;T:126437486;N:57705 76       126685179 75658897 75455501 126437486 57705 SRX21296458 SRS18545736 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.79163   0.52938   0.73304   0.48118   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25105 25105 SRR25567717 SRX21296458 SRS18545736 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 WT/Het replicate 1 RNAseq GSM7696243   source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 WT/Het replicate 1 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. wild type and heterozygous siblings   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696243 GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq GSM7696243 r1 GSM7696243 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     410-Tie1-WT-HT1_S1_L003_R1_001.fastq.gz fastq 419693128.0 5522278.0 GSM7696243 r3 0:76 A:131491219;C:78551884;G:78434940;T:131179828;N:35257 76       131491219 78551884 78434940 131179828 35257 SRX21296458 SRS18545736 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.79077   0.52836   0.73419   0.48215   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
25106 25106 SRR25567718 SRX21296458 SRS18545736 SRP453968 PRJNA1003386 Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish GSE240329 Transcriptome Analysis To investigate what kind of gene expression is regulated downstream of Tie1 signaling we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration proliferation and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.   pubmed:38742432   EC tie1 WT/Het replicate 1 RNAseq GSM7696243   source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing EC tie1 WT/Het replicate 1 RNAseq RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1 and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample. wild type and heterozygous siblings   Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed GSM7696243 GSM7696243: EC tie1 WT/Het replicate 1 RNAseq; Danio rerio; RNA Seq GSM7696243 r1 GSM7696243 1 Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 / zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS 0.8 mM calcium chloride 50 U/ml penicillin and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 / embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel 740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs E7760   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP453968     410-Tie1-WT-HT1_S1_L004_R1_001.fastq.gz fastq 418155268.0 5502043.0 GSM7696243 r4 0:76 A:130978746;C:78285682;G:78062725;T:130798846;N:29269 76       130978746 78285682 78062725 130798846 29269 SRX21296458 SRS18545736 SRA1688627 Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.78728   0.52541   0.73484   0.48813   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified nebnext sc single_cell_plate smartseq   Japan 2023-08-08 Pharyngula Embryo Multi-tissue Multi-system
29808 29808 SRR27450807 SRX23122487 SRS20076037 SRP482328 PRJNA1061565 Akt is the main kinase mediating the embryonic specification of artery cells GSE252648 Transcriptome Analysis This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.   pubmed:39101673   Zebrafish EC 24hpf Aktmutant GSM8004755   source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant|geo loc name:missing|collection date:missing Zebrafish EC 24hpf Aktmutant The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix FAC sorted cells No treatments Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics Normal zebrafish growth condition tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant GSM8004755 GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq GSM8004755 r1 GSM8004755 1 Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP482328   loader:fastq load.py mu1-23-19_DRT_S2_L001_I1_001.fastq.gz mu1-23-19_DRT_S2_L001_R1_001.fastq.gz mu1-23-19_DRT_S2_L001_R2_001.fastq.gz fastq fastq fastq 23281472741.0 183318683.0 GSM8004755 r1 0:8 1:28 2:91 A:4703583066;C:3702175361;G:3998796644;T:4271932211;N:5512871 8 28 91   4703583066 3702175361 3998796644 4271932211 5512871 SRX23122487 SRS20076037 SRA1780571 Nicoli lab, School of Medicine, Yale University Nicoli lab, School of Medicine, Yale University                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-05 Pharyngula Embryo Multi-tissue Multi-system
29809 29809 SRR27450808 SRX23122487 SRS20076037 SRP482328 PRJNA1061565 Akt is the main kinase mediating the embryonic specification of artery cells GSE252648 Transcriptome Analysis This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.   pubmed:39101673   Zebrafish EC 24hpf Aktmutant GSM8004755   source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant|geo loc name:missing|collection date:missing Zebrafish EC 24hpf Aktmutant The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix FAC sorted cells No treatments Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics Normal zebrafish growth condition tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant GSM8004755 GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq GSM8004755 r1 GSM8004755 1 Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP482328   loader:fastq load.py mu1-23-19_DRT_S2_L002_I1_001.fastq.gz mu1-23-19_DRT_S2_L002_R1_001.fastq.gz mu1-23-19_DRT_S2_L002_R2_001.fastq.gz fastq fastq fastq 21009317138.0 165427694.0 GSM8004755 r2 0:8 1:28 2:91 A:4231955850;C:3363548064;G:3603913589;T:3849411287;N:5091364 8 28 91   4231955850 3363548064 3603913589 3849411287 5091364 SRX23122487 SRS20076037 SRA1780571 Nicoli lab, School of Medicine, Yale University Nicoli lab, School of Medicine, Yale University                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-05 Pharyngula Embryo Multi-tissue Multi-system
29810 29810 SRR27450809 SRX23122486 SRS20076036 SRP482328 PRJNA1061565 Akt is the main kinase mediating the embryonic specification of artery cells GSE252648 Transcriptome Analysis This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.   pubmed:39101673   Zebrafish EC 24hpf WT GSM8004754   source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing Zebrafish EC 24hpf WT The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix FAC sorted cells No treatments Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics Normal zebrafish growth condition tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT GSM8004754 GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq GSM8004754 r1 GSM8004754 1 Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP482328   loader:fastq load.py wt1-23-19_DRT_S1_L001_I1_001.fastq.gz wt1-23-19_DRT_S1_L001_R1_001.fastq.gz wt1-23-19_DRT_S1_L001_R2_001.fastq.gz fastq fastq fastq 22261273232.0 175285616.0 GSM8004754 r1 0:8 1:28 2:91 A:4475749188;C:3578353646;G:3836029871;T:4055646794;N:5211557 8 28 91   4475749188 3578353646 3836029871 4055646794 5211557 SRX23122486 SRS20076036 SRA1780571 Nicoli lab, School of Medicine, Yale University Nicoli lab, School of Medicine, Yale University                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-05 Pharyngula Embryo Multi-tissue Multi-system
29811 29811 SRR27450810 SRX23122486 SRS20076036 SRP482328 PRJNA1061565 Akt is the main kinase mediating the embryonic specification of artery cells GSE252648 Transcriptome Analysis This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.   pubmed:39101673   Zebrafish EC 24hpf WT GSM8004754   source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing Zebrafish EC 24hpf WT The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix FAC sorted cells No treatments Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics Normal zebrafish growth condition tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT GSM8004754 GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq GSM8004754 r1 GSM8004754 1 Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP482328   loader:fastq load.py wt1-23-19_DRT_S1_L002_I1_001.fastq.gz wt1-23-19_DRT_S1_L002_R1_001.fastq.gz wt1-23-19_DRT_S1_L002_R2_001.fastq.gz fastq fastq fastq 20084395188.0 158144844.0 GSM8004754 r2 0:8 1:28 2:91 A:4028678970;C:3250176957;G:3455600305;T:3651884457;N:4840115 8 28 91   4028678970 3250176957 3455600305 3651884457 4840115 SRX23122486 SRS20076036 SRA1780571 Nicoli lab, School of Medicine, Yale University Nicoli lab, School of Medicine, Yale University                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-01-05 Pharyngula Embryo Multi-tissue Multi-system
29909 29909 SRR27592934 SRX23261746 SRS20163710 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep11 GSM8020192   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep11 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020192 GSM8020192: deaf1 2 dpf rep11; Danio rerio; RNA Seq GSM8020192 r1 GSM8020192 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D28_S56_R1_001.fastq.gz fastq 4475806200.0 44758062.0 GSM8020192 r1 0:100 A:1106171674;C:1156870042;G:1092472583;T:1120212338;N:79563 100       1106171674 1156870042 1092472583 1120212338 79563 SRX23261746 SRS20163710 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29910 29910 SRR27592935 SRX23261745 SRS20163711 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep10 GSM8020191   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep10 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020191 GSM8020191: deaf1 2 dpf rep10; Danio rerio; RNA Seq GSM8020191 r1 GSM8020191 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D27_S55_R1_001.fastq.gz fastq 4001586700.0 40015867.0 GSM8020191 r1 0:100 A:1000059012;C:1020300240;G:981249122;T:999909425;N:68901 100       1000059012 1020300240 981249122 999909425 68901 SRX23261745 SRS20163711 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29911 29911 SRR27592936 SRX23261744 SRS20163709 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep9 GSM8020190   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep9 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020190 GSM8020190: deaf1 2 dpf rep9; Danio rerio; RNA Seq GSM8020190 r1 GSM8020190 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D26_S54_R1_001.fastq.gz fastq 3716740300.0 37167403.0 GSM8020190 r1 0:100 A:930732486;C:940157658;G:908687307;T:937097122;N:65727 100       930732486 940157658 908687307 937097122 65727 SRX23261744 SRS20163709 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29912 29912 SRR27592937 SRX23261743 SRS20163708 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep8 GSM8020189   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep8 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020189 GSM8020189: deaf1 2 dpf rep8; Danio rerio; RNA Seq GSM8020189 r1 GSM8020189 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D25_S53_R1_001.fastq.gz fastq 3741485000.0 37414850.0 GSM8020189 r1 0:100 A:929440558;C:958986044;G:914039968;T:938952561;N:65869 100       929440558 958986044 914039968 938952561 65869 SRX23261743 SRS20163708 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29913 29913 SRR27592938 SRX23261742 SRS20163707 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep7 GSM8020188   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep7 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020188 GSM8020188: deaf1 2 dpf rep7; Danio rerio; RNA Seq GSM8020188 r1 GSM8020188 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D24_S52_R1_001.fastq.gz fastq 2971991400.0 29719914.0 GSM8020188 r1 0:100 A:738636815;C:755836125;G:729168292;T:748297854;N:52314 100       738636815 755836125 729168292 748297854 52314 SRX23261742 SRS20163707 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29914 29914 SRR27592939 SRX23261741 SRS20163706 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep6 GSM8020187   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep6 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020187 GSM8020187: deaf1 2 dpf rep6; Danio rerio; RNA Seq GSM8020187 r1 GSM8020187 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D23_S51_R1_001.fastq.gz fastq 4134397800.0 41343978.0 GSM8020187 r1 0:100 A:1032735373;C:1051188374;G:1016197596;T:1034203095;N:73362 100       1032735373 1051188374 1016197596 1034203095 73362 SRX23261741 SRS20163706 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29915 29915 SRR27592940 SRX23261740 SRS20163705 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep5 GSM8020186   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep5 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020186 GSM8020186: deaf1 2 dpf rep5; Danio rerio; RNA Seq GSM8020186 r1 GSM8020186 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D22_S50_R1_001.fastq.gz fastq 3631624500.0 36316245.0 GSM8020186 r1 0:100 A:901094303;C:929956244;G:893844528;T:906664233;N:65192 100       901094303 929956244 893844528 906664233 65192 SRX23261740 SRS20163705 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29916 29916 SRR27592941 SRX23261739 SRS20163704 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep4 GSM8020185   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep4 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020185 GSM8020185: deaf1 2 dpf rep4; Danio rerio; RNA Seq GSM8020185 r1 GSM8020185 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D21_S49_R1_001.fastq.gz fastq 3349609200.0 33496092.0 GSM8020185 r1 0:100 A:835857971;C:854981364;G:824035698;T:834673793;N:60374 100       835857971 854981364 824035698 834673793 60374 SRX23261739 SRS20163704 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29917 29917 SRR27592942 SRX23261738 SRS20163703 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep3 GSM8020184   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep3 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous GSM8020184 GSM8020184: deaf1 2 dpf rep3; Danio rerio; RNA Seq GSM8020184 r1 GSM8020184 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-het_D20_S48_R1_001.fastq.gz fastq 3371713300.0 33717133.0 GSM8020184 r1 0:100 A:839050016;C:857965663;G:828869795;T:845766740;N:61086 100       839050016 857965663 828869795 845766740 61086 SRX23261738 SRS20163703 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29918 29918 SRR27592943 SRX23261737 SRS20163701 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep2 GSM8020183   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep2 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous GSM8020183 GSM8020183: deaf1 2 dpf rep2; Danio rerio; RNA Seq GSM8020183 r1 GSM8020183 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-het_D18_S46_R1_001.fastq.gz fastq 3756501100.0 37565011.0 GSM8020183 r1 0:100 A:938612608;C:949004833;G:927692516;T:941125085;N:66058 100       938612608 949004833 927692516 941125085 66058 SRX23261737 SRS20163701 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29919 29919 SRR27592944 SRX23261736 SRS20163702 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep1 GSM8020182   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep1 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous GSM8020182 GSM8020182: deaf1 2 dpf rep1; Danio rerio; RNA Seq GSM8020182 r1 GSM8020182 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-het_D17_S45_R1_001.fastq.gz fastq 3378074100.0 33780741.0 GSM8020182 r1 0:100 A:839320911;C:859028175;G:836373251;T:843291522;N:60241 100       839320911 859028175 836373251 843291522 60241 SRX23261736 SRS20163702 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29920 29920 SRR27592945 SRX23261735 SRS20163699 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep13 GSM8020181   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep13 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types GSM8020181 GSM8020181: deaf1 t238p 2 dpf rep13; Danio rerio; RNA Seq GSM8020181 r1 GSM8020181 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-wt_ST4.fastq.gz fastq 2522881653.0 33818740.0 GSM8020181 r1 0:74.60 A:655207900;C:616856238;G:613068980;T:637525231;N:223304 74       655207900 616856238 613068980 637525231 223304 SRX23261735 SRS20163699 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29921 29921 SRR27592946 SRX23261734 SRS20163698 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep12 GSM8020180   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep12 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types GSM8020180 GSM8020180: deaf1 t238p 2 dpf rep12; Danio rerio; RNA Seq GSM8020180 r1 GSM8020180 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-wt_ST3.fastq.gz fastq 3232696302.0 43332777.0 GSM8020180 r1 0:74.60 A:838706781;C:792017578;G:780975426;T:820709157;N:287360 74       838706781 792017578 780975426 820709157 287360 SRX23261734 SRS20163698 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29922 29922 SRR27592947 SRX23261733 SRS20163700 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep11 GSM8020179   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep11 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types GSM8020179 GSM8020179: deaf1 t238p 2 dpf rep11; Danio rerio; RNA Seq GSM8020179 r1 GSM8020179 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-wt_ST2.fastq.gz fastq 3105671470.0 41634840.0 GSM8020179 r1 0:74.59 A:797054679;C:770109006;G:759275000;T:778955169;N:277616 74       797054679 770109006 759275000 778955169 277616 SRX23261733 SRS20163700 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29923 29923 SRR27592948 SRX23261732 SRS20163697 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep10 GSM8020178   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep10 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types GSM8020178 GSM8020178: deaf1 t238p 2 dpf rep10; Danio rerio; RNA Seq GSM8020178 r1 GSM8020178 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-wt_ST1.fastq.gz fastq 3499217864.0 46905154.0 GSM8020178 r1 0:74.60 A:893360259;C:869418642;G:860403580;T:875711902;N:323481 74       893360259 869418642 860403580 875711902 323481 SRX23261732 SRS20163697 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29924 29924 SRR27592949 SRX23261731 SRS20163696 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep9 GSM8020177   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep9 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous GSM8020177 GSM8020177: deaf1 t238p 2 dpf rep9; Danio rerio; RNA Seq GSM8020177 r1 GSM8020177 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-hom_ST8.fastq.gz fastq 3268771798.0 43820118.0 GSM8020177 r1 0:74.60 A:847366551;C:800849702;G:791226044;T:829037606;N:291895 74       847366551 800849702 791226044 829037606 291895 SRX23261731 SRS20163696 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29925 29925 SRR27592950 SRX23261730 SRS20163695 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep8 GSM8020176   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep8 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous GSM8020176 GSM8020176: deaf1 t238p 2 dpf rep8; Danio rerio; RNA Seq GSM8020176 r1 GSM8020176 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-hom_ST7.fastq.gz fastq 2027174325.0 27178466.0 GSM8020176 r1 0:74.59 A:525317640;C:498055852;G:491357881;T:512263813;N:179139 74       525317640 498055852 491357881 512263813 179139 SRX23261730 SRS20163695 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29926 29926 SRR27592951 SRX23261729 SRS20163694 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep7 GSM8020175   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep7 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous GSM8020175 GSM8020175: deaf1 t238p 2 dpf rep7; Danio rerio; RNA Seq GSM8020175 r1 GSM8020175 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-hom_ST6.fastq.gz fastq 2787340348.0 37363599.0 GSM8020175 r1 0:74.60 A:722896986;C:681138747;G:674833627;T:708219281;N:251707 74       722896986 681138747 674833627 708219281 251707 SRX23261729 SRS20163694 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29927 29927 SRR27592952 SRX23261728 SRS20163693 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep6 GSM8020174   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep6 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous GSM8020174 GSM8020174: deaf1 t238p 2 dpf rep6; Danio rerio; RNA Seq GSM8020174 r1 GSM8020174 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-hom_ST5.fastq.gz fastq 2977171544.0 39908640.0 GSM8020174 r1 0:74.60 A:770250088;C:731344480;G:721594408;T:753713587;N:268981 74       770250088 731344480 721594408 753713587 268981 SRX23261728 SRS20163693 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29928 29928 SRR27592953 SRX23261727 SRS20163692 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep5 GSM8020173   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep5 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020173 GSM8020173: deaf1 t238p 2 dpf rep5; Danio rerio; RNA Seq GSM8020173 r1 GSM8020173 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST9.fastq.gz fastq 2546529762.0 34141024.0 GSM8020173 r1 0:74.59 A:665391714;C:618921995;G:614059292;T:647931593;N:225168 74       665391714 618921995 614059292 647931593 225168 SRX23261727 SRS20163692 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29929 29929 SRR27592954 SRX23261726 SRS20163691 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep4 GSM8020172   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep4 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020172 GSM8020172: deaf1 t238p 2 dpf rep4; Danio rerio; RNA Seq GSM8020172 r1 GSM8020172 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST13.fastq.gz fastq 3176861738.0 42588753.0 GSM8020172 r1 0:74.59 A:831927955;C:768758728;G:763547713;T:812339162;N:288180 74       831927955 768758728 763547713 812339162 288180 SRX23261726 SRS20163691 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29930 29930 SRR27592955 SRX23261725 SRS20163690 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep3 GSM8020171   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep3 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020171 GSM8020171: deaf1 t238p 2 dpf rep3; Danio rerio; RNA Seq GSM8020171 r1 GSM8020171 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST12.fastq.gz fastq 1136232560.0 15234548.0 GSM8020171 r1 0:74.58 A:297385645;C:276022399;G:273402666;T:289320311;N:101539 74       297385645 276022399 273402666 289320311 101539 SRX23261725 SRS20163690 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29931 29931 SRR27592956 SRX23261724 SRS20163689 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep2 GSM8020170   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep2 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020170 GSM8020170: deaf1 t238p 2 dpf rep2; Danio rerio; RNA Seq GSM8020170 r1 GSM8020170 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST11.fastq.gz fastq 2735749019.0 36680185.0 GSM8020170 r1 0:74.58 A:721197113;C:659588175;G:652875625;T:701848626;N:239480 74       721197113 659588175 652875625 701848626 239480 SRX23261724 SRS20163689 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29932 29932 SRR27592957 SRX23261723 SRS20163688 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep1 GSM8020169   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep1 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020169 GSM8020169: deaf1 t238p 2 dpf rep1; Danio rerio; RNA Seq GSM8020169 r1 GSM8020169 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST10.fastq.gz fastq 3369699901.0 45178398.0 GSM8020169 r1 0:74.59 A:883991145;C:814741172;G:809532162;T:861133903;N:301519 74       883991145 814741172 809532162 861133903 301519 SRX23261723 SRS20163688 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29947 29947 SRR27592972 SRX23261708 SRS20163673 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep13 GSM8020168   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep13 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020168 GSM8020168: deaf1 c207y 2 dpf rep13; Danio rerio; RNA Seq GSM8020168 r1 GSM8020168 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_B2_S14_R1_001.fastq.gz fastq 2963811367.0 29344667.0 GSM8020168 r1 0:101 A:803333990;C:685431342;G:677569210;T:797384558;N:92267 101       803333990 685431342 677569210 797384558 92267 SRX23261708 SRS20163673 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29948 29948 SRR27592973 SRX23261707 SRS20163672 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep12 GSM8020167   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep12 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020167 GSM8020167: deaf1 c207y 2 dpf rep12; Danio rerio; RNA Seq GSM8020167 r1 GSM8020167 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_B1_S13_R1_001.fastq.gz fastq 3184165289.0 31526389.0 GSM8020167 r1 0:101 A:847208990;C:751109498;G:736855605;T:848892893;N:98303 101       847208990 751109498 736855605 848892893 98303 SRX23261707 SRS20163672 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29949 29949 SRR27592974 SRX23261706 SRS20163671 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep11 GSM8020166   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep11 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020166 GSM8020166: deaf1 c207y 2 dpf rep11; Danio rerio; RNA Seq GSM8020166 r1 GSM8020166 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_A12_S12_R1_001.fastq.gz fastq 3115838183.0 30849883.0 GSM8020166 r1 0:101 A:846133299;C:724401184;G:709966835;T:835240904;N:95961 101       846133299 724401184 709966835 835240904 95961 SRX23261706 SRS20163671 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29950 29950 SRR27592975 SRX23261705 SRS20163670 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep10 GSM8020165   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep10 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020165 GSM8020165: deaf1 c207y 2 dpf rep10; Danio rerio; RNA Seq GSM8020165 r1 GSM8020165 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_A11_S11_R1_001.fastq.gz fastq 2767984184.0 27405784.0 GSM8020165 r1 0:101 A:753665483;C:638171516;G:626255827;T:749805524;N:85834 101       753665483 638171516 626255827 749805524 85834 SRX23261705 SRS20163670 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29951 29951 SRR27592976 SRX23261704 SRS20163669 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep9 GSM8020164   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep9 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020164 GSM8020164: deaf1 c207y 2 dpf rep9; Danio rerio; RNA Seq GSM8020164 r1 GSM8020164 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_A10_S10_R1_001.fastq.gz fastq 5417478400.0 53638400.0 GSM8020164 r1 0:101 A:1459560082;C:1269220844;G:1235271759;T:1453256921;N:168794 101       1459560082 1269220844 1235271759 1453256921 168794 SRX23261704 SRS20163669 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29952 29952 SRR27592977 SRX23261703 SRS20163668 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep8 GSM8020163   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep8 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous GSM8020163 GSM8020163: deaf1 c207y 2 dpf rep8; Danio rerio; RNA Seq GSM8020163 r1 GSM8020163 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-hom_A9_S9_R1_001.fastq.gz fastq 2417886167.0 23939467.0 GSM8020163 r1 0:101 A:657342317;C:558713775;G:547590726;T:654164599;N:74750 101       657342317 558713775 547590726 654164599 74750 SRX23261703 SRS20163668 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29953 29953 SRR27592978 SRX23261702 SRS20163667 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep7 GSM8020162   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep7 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous GSM8020162 GSM8020162: deaf1 c207y 2 dpf rep7; Danio rerio; RNA Seq GSM8020162 r1 GSM8020162 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-hom_A8_S8_R1_001.fastq.gz fastq 3601305288.0 35656488.0 GSM8020162 r1 0:101 A:974139857;C:839029639;G:822572729;T:965450738;N:112325 101       974139857 839029639 822572729 965450738 112325 SRX23261702 SRS20163667 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29954 29954 SRR27592979 SRX23261701 SRS20163666 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep6 GSM8020161   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep6 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous GSM8020161 GSM8020161: deaf1 c207y 2 dpf rep6; Danio rerio; RNA Seq GSM8020161 r1 GSM8020161 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-hom_A6_S6_R1_001.fastq.gz fastq 2545549965.0 25203465.0 GSM8020161 r1 0:101 A:689302325;C:596907356;G:578571204;T:680690103;N:78977 101       689302325 596907356 578571204 680690103 78977 SRX23261701 SRS20163666 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29955 29955 SRR27592980 SRX23261700 SRS20163665 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep5 GSM8020160   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep5 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020160 GSM8020160: deaf1 c207y 2 dpf rep5; Danio rerio; RNA Seq GSM8020160 r1 GSM8020160 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A5_S5_R1_001.fastq.gz fastq 3102857158.0 30721358.0 GSM8020160 r1 0:101 A:850838897;C:712670459;G:688515516;T:850736210;N:96076 101       850838897 712670459 688515516 850736210 96076 SRX23261700 SRS20163665 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29956 29956 SRR27592981 SRX23261699 SRS20163664 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep4 GSM8020159   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep4 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020159 GSM8020159: deaf1 c207y 2 dpf rep4; Danio rerio; RNA Seq GSM8020159 r1 GSM8020159 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A4_S4_R1_001.fastq.gz fastq 3415651633.0 33818333.0 GSM8020159 r1 0:101 A:933225760;C:786732356;G:770845968;T:924742081;N:105468 101       933225760 786732356 770845968 924742081 105468 SRX23261699 SRS20163664 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29957 29957 SRR27592982 SRX23261698 SRS20163663 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep3 GSM8020158   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep3 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020158 GSM8020158: deaf1 c207y 2 dpf rep3; Danio rerio; RNA Seq GSM8020158 r1 GSM8020158 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A3_S3_R1_001.fastq.gz fastq 3429734972.0 33957772.0 GSM8020158 r1 0:101 A:920850547;C:802940416;G:790735026;T:915103526;N:105457 101       920850547 802940416 790735026 915103526 105457 SRX23261698 SRS20163663 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29958 29958 SRR27592983 SRX23261697 SRS20163662 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep2 GSM8020157   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep2 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020157 GSM8020157: deaf1 c207y 2 dpf rep2; Danio rerio; RNA Seq GSM8020157 r1 GSM8020157 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A2_S2_R1_001.fastq.gz fastq 2810870602.0 27830402.0 GSM8020157 r1 0:101 A:742011214;C:673773327;G:656344142;T:738655690;N:86229 101       742011214 673773327 656344142 738655690 86229 SRX23261697 SRS20163662 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29959 29959 SRR27592984 SRX23261696 SRS20163661 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep1 GSM8020156   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep1 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020156 GSM8020156: deaf1 c207y 2 dpf rep1; Danio rerio; RNA Seq GSM8020156 r1 GSM8020156 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A1_S1_R1_001.fastq.gz fastq 4234517819.0 41925919.0 GSM8020156 r1 0:101 A:1104853000;C:1023572758;G:1001000314;T:1104961067;N:130680 101       1104853000 1023572758 1001000314 1104961067 130680 SRX23261696 SRS20163661 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29993 29993 SRR27593018 SRX23261662 SRS20163627 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep13 GSM8020194   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep13 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020194 GSM8020194: deaf1 2 dpf rep13; Danio rerio; RNA Seq GSM8020194 r1 GSM8020194 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D30_S58_R1_001.fastq.gz fastq 4417470800.0 44174708.0 GSM8020194 r1 0:100 A:1088757969;C:1142271720;G:1089301455;T:1097060536;N:79120 100       1088757969 1142271720 1089301455 1097060536 79120 SRX23261662 SRS20163627 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29994 29994 SRR27593019 SRX23261661 SRS20163626 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep12 GSM8020193   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep12 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020193 GSM8020193: deaf1 2 dpf rep12; Danio rerio; RNA Seq GSM8020193 r1 GSM8020193 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D29_S57_R1_001.fastq.gz fastq 4218209500.0 42182095.0 GSM8020193 r1 0:100 A:1040374012;C:1082175747;G:1042489373;T:1053094232;N:76136 100       1040374012 1082175747 1042489373 1053094232 76136 SRX23261661 SRS20163626 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
33700 33700 SRR30599779 SRX26022472 SRS22594191 SRP531514 PRJNA1158727 CRISPR/Cas9 induced zebrafish mutants for ebf3a and dhx30 GSE276705 Transcriptome Analysis Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss however have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes including an overall smaller brain size particularly in the hypothalamus cerebellum and hindbrain. Brain function was also compromised with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae notable changes included significant downregulation of genes that mark olfactory sensory neurons the lateral line and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen. RNA for the 2 dpf RNA seq samples were collected in the same way but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.       ebf3a wt 2 dpf rep 2 GSM8504324   source name:upper body with eyes 15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing ebf3a wt 2 dpf rep 2 Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. upper body with eyes 15 20 embryos pooled   Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types GSM8504324 GSM8504324: ebf3a wt 2 dpf rep 2; Danio rerio; RNA Seq GSM8504324 r1 GSM8504324 1 Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     Ebf-WT-2-2dpf_R1_001.fastq.gz Ebf-WT-2-2dpf_R2_001.fastq.gz fastq fastq 22635570600.0 75451902.0 GSM8504324 r1 0:150 1:150 A:6279354286;C:5013138453;G:5250498169;T:6092284847;N:294845 150 150     6279354286 5013138453 5250498169 6092284847 294845 SRX26022472 SRS22594191 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33701 33701 SRR30599780 SRX26022471 SRS22594190 SRP531514 PRJNA1158727 CRISPR/Cas9 induced zebrafish mutants for ebf3a and dhx30 GSE276705 Transcriptome Analysis Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss however have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes including an overall smaller brain size particularly in the hypothalamus cerebellum and hindbrain. Brain function was also compromised with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae notable changes included significant downregulation of genes that mark olfactory sensory neurons the lateral line and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen. RNA for the 2 dpf RNA seq samples were collected in the same way but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.       ebf3a wt 2 dpf rep 1 GSM8504323   source name:upper body with eyes 15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing ebf3a wt 2 dpf rep 1 Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. upper body with eyes 15 20 embryos pooled   Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types GSM8504323 GSM8504323: ebf3a wt 2 dpf rep 1; Danio rerio; RNA Seq GSM8504323 r1 GSM8504323 1 Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     Ebf-WT-1-2dpf_R1_001.fastq.gz Ebf-WT-1-2dpf_R2_001.fastq.gz fastq fastq 19711425600.0 65704752.0 GSM8504323 r1 0:150 1:150 A:5541464229;C:4291380685;G:4497372769;T:5380954703;N:253214 150 150     5541464229 4291380685 4497372769 5380954703 253214 SRX26022471 SRS22594190 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33702 33702 SRR30599781 SRX26022470 SRS22594189 SRP531514 PRJNA1158727 CRISPR/Cas9 induced zebrafish mutants for ebf3a and dhx30 GSE276705 Transcriptome Analysis Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss however have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes including an overall smaller brain size particularly in the hypothalamus cerebellum and hindbrain. Brain function was also compromised with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae notable changes included significant downregulation of genes that mark olfactory sensory neurons the lateral line and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen. RNA for the 2 dpf RNA seq samples were collected in the same way but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.       ebf3a het 2 dpf rep 2 GSM8504322   source name:upper body with eyes 15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous|geo loc name:missing|collection date:missing ebf3a het 2 dpf rep 2 Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. upper body with eyes 15 20 embryos pooled   Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous GSM8504322 GSM8504322: ebf3a het 2 dpf rep 2; Danio rerio; RNA Seq GSM8504322 r1 GSM8504322 1 Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     Ebf-HET-2-2dpf_R1_001.fastq.gz Ebf-HET-2-2dpf_R2_001.fastq.gz fastq fastq 15108144300.0 50360481.0 GSM8504322 r1 0:150 1:150 A:4240605272;C:3297282748;G:3449975456;T:4120084716;N:196108 150 150     4240605272 3297282748 3449975456 4120084716 196108 SRX26022470 SRS22594189 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33703 33703 SRR30599782 SRX26022469 SRS22594188 SRP531514 PRJNA1158727 CRISPR/Cas9 induced zebrafish mutants for ebf3a and dhx30 GSE276705 Transcriptome Analysis Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss however have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes including an overall smaller brain size particularly in the hypothalamus cerebellum and hindbrain. Brain function was also compromised with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae notable changes included significant downregulation of genes that mark olfactory sensory neurons the lateral line and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen. RNA for the 2 dpf RNA seq samples were collected in the same way but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.       ebf3a het 2 dpf rep 1 GSM8504321   source name:upper body with eyes 15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous|geo loc name:missing|collection date:missing ebf3a het 2 dpf rep 1 Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. upper body with eyes 15 20 embryos pooled   Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous GSM8504321 GSM8504321: ebf3a het 2 dpf rep 1; Danio rerio; RNA Seq GSM8504321 r1 GSM8504321 1 Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     Ebf-HET-1-2dpf_R1_001.fastq.gz Ebf-HET-1-2dpf_R2_001.fastq.gz fastq fastq 16538340600.0 55127802.0 GSM8504321 r1 0:150 1:150 A:4633062848;C:3617047326;G:3792365071;T:4495647394;N:217961 150 150     4633062848 3617047326 3792365071 4495647394 217961 SRX26022469 SRS22594188 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33704 33704 SRR30599783 SRX26022468 SRS22594186 SRP531514 PRJNA1158727 CRISPR/Cas9 induced zebrafish mutants for ebf3a and dhx30 GSE276705 Transcriptome Analysis Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss however have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes including an overall smaller brain size particularly in the hypothalamus cerebellum and hindbrain. Brain function was also compromised with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae notable changes included significant downregulation of genes that mark olfactory sensory neurons the lateral line and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen. RNA for the 2 dpf RNA seq samples were collected in the same way but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.       ebf3a hom 2 dpf rep 2 GSM8504320   source name:upper body with eyes 15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing ebf3a hom 2 dpf rep 2 Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. upper body with eyes 15 20 embryos pooled   Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous GSM8504320 GSM8504320: ebf3a hom 2 dpf rep 2; Danio rerio; RNA Seq GSM8504320 r1 GSM8504320 1 Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     Ebf-HOMO-2-2dpf_R1_001.fastq.gz Ebf-HOMO-2-2dpf_R2_001.fastq.gz fastq fastq 14586421200.0 48621404.0 GSM8504320 r1 0:150 1:150 A:4099529019;C:3162437766;G:3348146726;T:3976118566;N:189123 150 150     4099529019 3162437766 3348146726 3976118566 189123 SRX26022468 SRS22594186 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33705 33705 SRR30599784 SRX26022467 SRS22594187 SRP531514 PRJNA1158727 CRISPR/Cas9 induced zebrafish mutants for ebf3a and dhx30 GSE276705 Transcriptome Analysis Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss however have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes including an overall smaller brain size particularly in the hypothalamus cerebellum and hindbrain. Brain function was also compromised with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae notable changes included significant downregulation of genes that mark olfactory sensory neurons the lateral line and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen. RNA for the 2 dpf RNA seq samples were collected in the same way but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.       ebf3a hom 2 dpf rep 1 GSM8504319   source name:upper body with eyes 15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing ebf3a hom 2 dpf rep 1 Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. upper body with eyes 15 20 embryos pooled   Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous GSM8504319 GSM8504319: ebf3a hom 2 dpf rep 1; Danio rerio; RNA Seq GSM8504319 r1 GSM8504319 1 Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     Ebf-HOMO-1-2dpf_R1_001.fastq.gz Ebf-HOMO-1-2dpf_R2_001.fastq.gz fastq fastq 14235405000.0 47451350.0 GSM8504319 r1 0:150 1:150 A:3937137116;C:3134793115;G:3336004625;T:3827286589;N:183555 150 150     3937137116 3134793115 3336004625 3827286589 183555 SRX26022467 SRS22594187 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
34551 34551 SRR32104356 SRX27449954 SRS23876475 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 3 GSM8751787   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 3 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751787 GSM8751787: 17hpf Positive CNC 3; Danio rerio; RNA Seq GSM8751787 r1 GSM8751787 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_3_22028_combined_filtered.fastq.gz fastq 5836253400.0 58362534.0 GSM8751787 r1 0:100 A:1666874971;C:1250406201;G:1263794016;T:1655113176;N:65036 100       1666874971 1250406201 1263794016 1655113176 65036 SRX27449954 SRS23876475 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
34552 34552 SRR32104357 SRX27449953 SRS23876474 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 2 GSM8751786   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 2 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751786 GSM8751786: 17hpf Positive CNC 2; Danio rerio; RNA Seq GSM8751786 r1 GSM8751786 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_2_21338_combined_filtered.fastq.gz fastq 2444486550.0 48889731.0 GSM8751786 r1 0:50 A:706384494;C:515182895;G:525593789;T:697319091;N:6281 50       706384494 515182895 525593789 697319091 6281 SRX27449953 SRS23876474 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
34553 34553 SRR32104358 SRX27449952 SRS23876472 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 1 GSM8751785   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 1 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751785 GSM8751785: 17hpf Positive CNC 1; Danio rerio; RNA Seq GSM8751785 r1 GSM8751785 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_1_21309_combined_filtered.fastq.gz fastq 3136080950.0 62721619.0 GSM8751785 r1 0:50 A:867446661;C:707750289;G:716376649;T:844460193;N:47158 50       867446661 707750289 716376649 844460193 47158 SRX27449952 SRS23876472 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
46219 46219 SRR6507314 SRX3595756 SRS2864146 SRP131267 PRJNA431425 tp53 deficiency causes a wide tumor spectrum and elevates embryonal rhabdomyosarcoma metastasis in zebrafish GSE109581 Transcriptome Analysis We generated tp53 deletion mutant zebrafish that spontaneously develop malignant peripheral nerve sheath tumors angiosarcomas germ cell tumors and an aggressive Natural Killer cell leukemia not previously reported in zebrafish. Each tumor type efficiently engrafted into syngeneic recipient zebrafish and shared gene expression signatures with predicted cells of origin. Overall design: We generated a complete null tp53 deletion allele in syngeneic CG1 strain zebrafish using TALEN endonucleases. The list of tumors spontaneously developed in these tp53del/del animals included malignant peripheral nerve sheath tumors MPNSTs angiosarcomas germ cell tumors and Natural Killer cell leukemia. We obtained 3 MPNSTs samples MPNST 1 MPNST 2 and MPNST 3 2 angiosarcoma samples Angiosarcoma 1 and Angiosarcoma 2 3 leukemia samples Leukemia 1 Leukemia 2 and Leukemia 3 and 1 sample of germ cell tumor GermCell 1. We also assessed the role of tp53 in kRASG12D induced human embryonal rhabdomyosarcoma ERMS using large scale cell transplantation assays and live fluorescent imaging over time. We obtained 3 ERMS samples ERMS 1 ERMS 2 and ERMS 3. All these tumor samples were compared to 3 background CG1 samples samples WholeFish 1 WholeFish 2 and WholeFish 3.   pubmed:30192230   GermCell 1 GSM2946795   tissue:germ cell tumor|genotype:CG1 tp53 homozygous mutant|tumor type:spontaneous|procedure:primary transplant GFP FACS sorted GermCell 1 Reads were aligned with STAR v2.4.0; PCR duplicates were removed with Picard v1.95 and reads aligning to ribosomal RNA were removed with RSeQC; gene counts were obtained from reads with an alignment quality of at least 10 using featureCounts and transformed to transcript per million TPM units. Genome build: GRCz10 Supplementary files format and content: Counts matrix provided as supplementary file. germ cell tumor Tissue was harvested using 90% PBS + 5% FBS. FACS sorting was performed to obtain tumor cell fraction with 85% purity and 90% viability. Total RNA was extracted using RLT buffer Qiagen and purified using RNeasy kit Qiagen as per manufacturer instructions Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit Animals were raised at 28 degrees celcius genotype:CG1 tp53 homozygous mutant|tumor type:spontaneous|procedure:primary transplant GFP FACS sorted GSM2946795 GSM2946795: GermCell 1; Danio rerio; RNA Seq GSM2946795   1 Total RNA was extracted using RLT buffer Qiagen and purified using RNeasy kit Qiagen as per manufacturer instructions Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit GEO Accession:GSM2946795 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP131267     GermCell_1.bam bam 3209068354.0 15886477.0 GSM2946795 r1 0:101 1:101 A:840598884;C:754814967;G:771176149;T:842218625;N:259729 101 101     840598884 754814967 771176149 842218625 259729 SRX3595756 SRS2864146 SRA652013 GEO Pathology, Massachusetts General Hospital 2 0.9446 0.94929 0.07879 0.07672 0.6518 0.65287 0.47991 0.48302 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2018-01-24 Undetermined Embryo Multi-tissue Multi-system
49611 49611 SRR7989641 SRX4820831 SRS3895222 SRP164769 PRJNA495391 Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling GSE121041 Transcriptome Analysis Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO   pubmed:30451830;pubmed:38570687   IWR 1 rep3 GSM3424991   source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf IWR 1 rep3 Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene brain endothelial cells   Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.   lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf GSM3424991 GSM3424991: IWR 1 rep3; Danio rerio; RNA Seq GSM3424991   1 Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech. GEO Accession:GSM3424991 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP164769     vanHollebeke_IWR_4_R1.fastq.gz fastq 2256000713.0 30503539.0 GSM3424991 r1 0:73.96 1:0 A:657293471;C:471495202;G:469388740;T:657813037;N:10263 73 0     657293471 471495202 469388740 657813037 10263 SRX4820831 SRS3895222 SRA791232 GEO MPI for heart and lung research 1 0.82891   0.22262   0.78894   0.52843   75   B   usable mapping rate illumina nextseq full_length cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-10-09 Pharyngula Embryo Multi-tissue Multi-system
49612 49612 SRR7989640 SRX4820830 SRS3895220 SRP164769 PRJNA495391 Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling GSE121041 Transcriptome Analysis Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO   pubmed:30451830;pubmed:38570687   IWR 1 rep2 GSM3424990   source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf IWR 1 rep2 Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene brain endothelial cells   Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.   lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf GSM3424990 GSM3424990: IWR 1 rep2; Danio rerio; RNA Seq GSM3424990   1 Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech. GEO Accession:GSM3424990 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP164769     vanHollebeke_IWR_3_R1.fastq.gz fastq 2320219813.0 31532406.0 GSM3424990 r1 0:73.58 1:0 A:660022378;C:501448817;G:498586533;T:660148405;N:13680 73 0     660022378 501448817 498586533 660148405 13680 SRX4820830 SRS3895220 SRA791232 GEO MPI for heart and lung research 1 0.76766   0.17893   0.78206   0.5236   74   B   usable mapping rate illumina nextseq full_length cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-10-09 Pharyngula Embryo Multi-tissue Multi-system
49613 49613 SRR7989639 SRX4820829 SRS3895221 SRP164769 PRJNA495391 Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling GSE121041 Transcriptome Analysis Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO   pubmed:30451830;pubmed:38570687   IWR 1 rep1 GSM3424989   source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf IWR 1 rep1 Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene brain endothelial cells   Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.   lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf GSM3424989 GSM3424989: IWR 1 rep1; Danio rerio; RNA Seq GSM3424989   1 Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech. GEO Accession:GSM3424989 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP164769     vanHollebeke_IWR_1_R1.fastq.gz fastq 3130301804.0 42242865.0 GSM3424989 r1 0:74.10 1:0 A:906281071;C:658248293;G:654046147;T:911712569;N:13724 74 0     906281071 658248293 654046147 911712569 13724 SRX4820829 SRS3895221 SRA791232 GEO MPI for heart and lung research 1 0.83335   0.2301   0.77703   0.51424   75   B   usable mapping rate illumina nextseq full_length cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-10-09 Pharyngula Embryo Multi-tissue Multi-system
49614 49614 SRR7989638 SRX4820828 SRS3895223 SRP164769 PRJNA495391 Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling GSE121041 Transcriptome Analysis Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO   pubmed:30451830;pubmed:38570687   DMSO rep3 GSM3424988   source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf DMSO rep3 Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene brain endothelial cells   Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.   lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf GSM3424988 GSM3424988: DMSO rep3; Danio rerio; RNA Seq GSM3424988   1 Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech. GEO Accession:GSM3424988 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP164769     vanHollebeke_WT_3_R1.fastq.gz fastq 2942028868.0 39840018.0 GSM3424988 r1 0:73.85 1:0 A:849808636;C:623040120;G:619275913;T:849871928;N:32271 73 0     849808636 623040120 619275913 849871928 32271 SRX4820828 SRS3895223 SRA791232 GEO MPI for heart and lung research 1 0.83348   0.20415   0.79147   0.51054   74   B   usable mapping rate illumina nextseq full_length cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-10-09 Pharyngula Embryo Multi-tissue Multi-system
49615 49615 SRR7989637 SRX4820827 SRS3895219 SRP164769 PRJNA495391 Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling GSE121041 Transcriptome Analysis Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO   pubmed:30451830;pubmed:38570687   DMSO rep2 GSM3424987   source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf DMSO rep2 Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene brain endothelial cells   Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.   lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf GSM3424987 GSM3424987: DMSO rep2; Danio rerio; RNA Seq GSM3424987   1 Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech. GEO Accession:GSM3424987 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP164769     vanHollebeke_WT_2_R1.fastq.gz fastq 2807935583.0 38002656.0 GSM3424987 r1 0:73.89 1:0 A:815631502;C:589381721;G:586257915;T:816652021;N:12424 73 0     815631502 589381721 586257915 816652021 12424 SRX4820827 SRS3895219 SRA791232 GEO MPI for heart and lung research 1 0.84347   0.20267   0.77419   0.51656   75   B   usable mapping rate illumina nextseq full_length cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-10-09 Pharyngula Embryo Multi-tissue Multi-system
49616 49616 SRR7989636 SRX4820826 SRS3895218 SRP164769 PRJNA495391 Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling GSE121041 Transcriptome Analysis Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO   pubmed:30451830;pubmed:38570687   DMSO rep1 GSM3424986   source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf DMSO rep1 Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene brain endothelial cells   Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.   lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf GSM3424986 GSM3424986: DMSO rep1; Danio rerio; RNA Seq GSM3424986   1 Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech. GEO Accession:GSM3424986 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP164769     vanHollebeke_WT_1_R1.fastq.gz fastq 2675908817.0 36130876.0 GSM3424986 r1 0:74.06 1:0 A:789957205;C:549799082;G:546545868;T:789594811;N:11851 74 0     789957205 549799082 546545868 789594811 11851 SRX4820826 SRS3895218 SRA791232 GEO MPI for heart and lung research 1 0.90594   0.2159   0.76765   0.50407   75   B   usable mapping rate illumina nextseq full_length cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-10-09 Pharyngula Embryo Multi-tissue Multi-system
53493 53493 SRR9881612 SRX6634133 SRS5205093 SRP217216 PRJNA558070 N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells GSE135246 Transcriptome Analysis Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds   pubmed:33273096   223mut 27hpf EC1 GSM3996907   source name:endothelial cell|tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303|genotype:223mut 223mut 27hpf EC1 The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition. endothelial cell   Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1 Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473. tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303|genotype:223mut GSM3996907 GSM3996907: 223mut 27hpf EC1; Danio rerio; RNA Seq GSM3996907   1 Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1 GEO Accession:GSM3996907 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP217216     Mut_pssorted_genome_bam.bam 10X Genomics bam file 31174899854.0 318111223.0 GSM3996907 r1 0:98 A:8464403532;C:7291172763;G:7282393533;T:8131647604;N:5282422 98       8464403532 7291172763 7282393533 8131647604 5282422 SRX6634133 SRS5205093 SRA930499 GEO Internal Medicine, Yale University 1 0.92745   0.05306   0.84502   0.46383   98   B   usable mapping rate illumina hiseq_era unknown small_rna unknown sc single_cell_droplet 10x   United States 2019-08-01 Pharyngula Embryo Multi-tissue Multi-system
53494 53494 SRR9881611 SRX6634132 SRS5205092 SRP217216 PRJNA558070 N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells GSE135246 Transcriptome Analysis Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds   pubmed:33273096   wildtype 27hpf EC1 GSM3996906   source name:endothelial cell|tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896|genotype:wildtype wildtype 27hpf EC1 The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition. endothelial cell   Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1 Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473. tissue:trunk endothelium|cell type:endothelial cell|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896|genotype:wildtype GSM3996906 GSM3996906: wildtype 27hpf EC1; Danio rerio; RNA Seq GSM3996906   1 Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1 GEO Accession:GSM3996906 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP217216     WT_pssorted_genome_bam.bam 10X Genomics bam file 26866951370.0 274152565.0 GSM3996906 r1 0:98 A:7373453026;C:6169004304;G:6196779570;T:7121490110;N:6224360 98       7373453026 6169004304 6196779570 7121490110 6224360 SRX6634132 SRS5205092 SRA930499 GEO Internal Medicine, Yale University 1 0.93015   0.0602   0.83853   0.4683   98   B   usable mapping rate illumina hiseq_era unknown small_rna unknown sc single_cell_droplet 10x   United States 2019-08-01 Pharyngula Embryo Multi-tissue Multi-system
53504 53504 SRR9879915 SRX6632436 SRS5202043 SRP217196 PRJNA558085 Zebrafish Danio rerio neural crest cell RNA sequencing GSE135237 Transcriptome Analysis RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.   pubmed:31495570   36hpfNCC rep3 GSM3996851   source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf 36hpfNCC rep3 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Neural crest cells from larval trunk 36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf GSM3996851 GSM3996851: 36hpfNCC rep3; Danio rerio; RNA Seq GSM3996851   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM3996851 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP217196     Sample3_S3_R1_001.fastq.gz Sample3_S3_R2_001.fastq.gz fastq fastq 5670363307.0 19001526.0 GSM3996851 r1 0:149.23 1:149.19 A:1557295113;C:1251445377;G:1252062318;T:1609175566;N:384933 149 149     1557295113 1251445377 1252062318 1609175566 384933 SRX6632436 SRS5202043 SRA930488 GEO Kucenas Lab, Biology, University of Virginia 2 0.85581 0.858 0.14092 0.14122 0.78784 0.7935 0.55466 0.55065 150 149 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2019-08-01 Pharyngula Embryo Multi-tissue Multi-system
53505 53505 SRR9879914 SRX6632435 SRS5202042 SRP217196 PRJNA558085 Zebrafish Danio rerio neural crest cell RNA sequencing GSE135237 Transcriptome Analysis RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.   pubmed:31495570   36hpfNCC rep2 GSM3996850   source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf 36hpfNCC rep2 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Neural crest cells from larval trunk 36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf GSM3996850 GSM3996850: 36hpfNCC rep2; Danio rerio; RNA Seq GSM3996850   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM3996850 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP217196     Sample2_S2_R2_001.fastq.gz Sample2_S2_R1_001.fastq.gz fastq fastq 7936706863.0 26647099.0 GSM3996850 r1 0:148.93 1:148.91 A:2180170247;C:1758018091;G:1758076526;T:2239839139;N:602860 148 148     2180170247 1758018091 1758076526 2239839139 602860 SRX6632435 SRS5202042 SRA930488 GEO Kucenas Lab, Biology, University of Virginia 2 0.85787 0.85726 0.14387 0.14335 0.7864 0.79123 0.55424 0.54305 150 149 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2019-08-01 Pharyngula Embryo Multi-tissue Multi-system
53506 53506 SRR9879913 SRX6632434 SRS5202041 SRP217196 PRJNA558085 Zebrafish Danio rerio neural crest cell RNA sequencing GSE135237 Transcriptome Analysis RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.   pubmed:31495570   36hpfNCC rep1 GSM3996849   source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf 36hpfNCC rep1 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Neural crest cells from larval trunk 36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf GSM3996849 GSM3996849: 36hpfNCC rep1; Danio rerio; RNA Seq GSM3996849   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM3996849 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP217196     Sample1_S1_R1_001.fastq.gz Sample1_S1_R2_001.fastq.gz fastq fastq 5567367667.0 18627261.0 GSM3996849 r1 0:149.46 1:149.42 A:1451891750;C:1299527629;G:1299734297;T:1515800229;N:413762 149 149     1451891750 1299527629 1299734297 1515800229 413762 SRX6632434 SRS5202041 SRA930488 GEO Kucenas Lab, Biology, University of Virginia 2 0.70717 0.70612 0.10919 0.10754 0.83366 0.83875 0.55253 0.55519 149 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2019-08-01 Pharyngula Embryo Multi-tissue Multi-system

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;