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95 rows where experiment.library_layout = "PAIRED", technology = "bulk" and tissue_curation = "Brain"

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devstage_curation 7

devstage_curation_coarse 5

experiment.library_selection 4

experiment.library_strategy 2

tissue_curation_coarse 1

tissue_curation 1

  • Brain · 95 ✖

technology 1

  • bulk · 95 ✖

experiment.platform 1

experiment.library_source 1

experiment.library_layout 1

  • PAIRED · 95 ✖
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
10391 10391 ERR8516975 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R 0:51 1:51 A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852 51 51     1077092958 949537387 955020348 1099432979 20556852 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.9053 0.9259 0.21658 0.22155 0.69369 0.69179 0.50726 0.50871 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10392 10392 ERR8516976 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R 0:51 1:51 A:972081222;C:890179393;G:888655698;T:998443264;N:18934747 51 51     972081222 890179393 888655698 998443264 18934747 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.86107 0.87807 0.22063 0.23029 0.70859 0.70561 0.51656 0.51946 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10393 10393 ERR8516977 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R 0:51 1:51 A:728798881;C:962223604;G:958876331;T:735449513;N:17094231 51 51     728798881 962223604 958876331 735449513 17094231 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.54616 0.55881 0.13313 0.14036 0.84295 0.84185 0.64193 0.59762 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10394 10394 ERR8516972 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R 0:51 1:51 A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786 51 51     837274632 1062368015 1049892288 853310517 19213786 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.5726 0.57788 0.13781 0.14082 0.80616 0.80452 0.61581 0.60389 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10395 10395 ERR8516973 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R 0:51 1:51 A:897813231;C:796012893;G:794839496;T:923696030;N:17221274 51 51     897813231 796012893 794839496 923696030 17221274 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.92095 0.94156 0.18892 0.20024 0.6901 0.68905 0.49377 0.50086 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10396 10396 ERR8516974 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R 0:51 1:51 A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248 51 51     951912827 1107150666 1086060798 973791571 20785248 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.63792 0.62667 0.18547 0.18671 0.78756 0.78549 0.59274 0.55478 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10397 10397 ERR8516969 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R 0:51 1:51 A:925784769;C:934445856;G:959155668;T:924080408;N:18878983 51 51     925784769 934445856 959155668 924080408 18878983 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.59503 0.61112 0.1947 0.20225 0.76512 0.76337 0.54584 0.54345 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10398 10398 ERR8516970 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R 0:51 1:51 A:991755033;C:864808531;G:892202564;T:992188806;N:18881958 51 51     991755033 864808531 892202564 992188806 18881958 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.86612 0.88689 0.26181 0.2728 0.7094 0.7091 0.53639 0.53906 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10399 10399 ERR8516971 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R 0:51 1:51 A:766707527;C:798667604;G:818782599;T:773280942;N:15938306 51 51     766707527 798667604 818782599 773280942 15938306 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.88811 0.92834 0.21869 0.22669 0.72878 0.72604 0.55598 0.57831 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10400 10400 ERR8516966 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R 0:51 1:51 A:774360373;C:720215184;G:719479745;T:796239200;N:15182374 51 51     774360373 720215184 719479745 796239200 15182374 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.79643 0.81194 0.25554 0.2603 0.72236 0.72021 0.51775 0.51678 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10401 10401 ERR8516967 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R 0:51 1:51 A:739921027;C:667375549;G:663864111;T:764302396;N:14288091 51 51     739921027 667375549 663864111 764302396 14288091 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.90817 0.92909 0.23387 0.24814 0.70088 0.69842 0.51238 0.51267 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10402 10402 ERR8516968 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X9_190227_A00421_38_AH7523DRXX_S49_R1_001.fastq.gz 15812X9_190227_A00421_38_AH7523DRXX_S49_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X9 190227 A00421 38 AH7523DRXX S49 R 0:51 1:51 A:882831441;C:935213418;G:957033335;T:879085993;N:18444957 51 51     882831441 935213418 957033335 879085993 18444957 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.76218 0.7682 0.18357 0.18521 0.74444 0.74272 0.46714 0.55518 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
11815 11815 ERR11799086 ERX11197445 ERS16222830 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 4 SAMEA114237385 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237385|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 4|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 4|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 4 p Sample 4 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R1.fq.gz so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R2.fq.gz fastq fastq 19305011730.0 95569365.0 E MTAB 13228:so zf94 VW4 MDMG7 CD45lo mhc2dab MGA S58 R 0:101 1:101 A:6768262250;C:3044091042;G:2847188942;T:6645295452;N:174044 101 101     6768262250 3044091042 2847188942 6645295452 174044 ERX11197445 ERS16222830 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.57007 0.5231 0.45597 0.40582 0.91579 0.91674 0.58257 0.5625 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11816 11816 ERR11799088 ERX11197447 ERS16222832 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 6 SAMEA114237387 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237387|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 6|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 6|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 6 p Sample 6 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R2.fq.gz so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R1.fq.gz fastq fastq 21028230098.0 104100149.0 E MTAB 13228:so zf94 VW6 MDMF8 CD45hi mhc2dab MACA S60 R 0:101 1:101 A:6738894716;C:4007335499;G:3664578692;T:6617229148;N:192043 101 101     6738894716 4007335499 3664578692 6617229148 192043 ERX11197447 ERS16222832 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.69217 0.69414 0.45934 0.4539 0.86423 0.86344 0.64485 0.62976 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11817 11817 ERR11799085 ERX11197444 ERS16222829 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 3 SAMEA114237384 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237384|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 3|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 3|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 3 p Sample 3 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R1.fq.gz so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R2.fq.gz fastq fastq 20720724286.0 102577843.0 E MTAB 13228:so zf94 VW3 MDMG1 CD45lo mhc2dab MGA S57 R 0:101 1:101 A:7221245295;C:3305546836;G:3154595537;T:7039147315;N:189303 101 101     7221245295 3305546836 3154595537 7039147315 189303 ERX11197444 ERS16222829 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.6027 0.56103 0.46397 0.41738 0.90536 0.90473 0.59858 0.59246 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11818 11818 ERR11799087 ERX11197446 ERS16222831 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 5 SAMEA114237386 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237386|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 5|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 5|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 5 p Sample 5 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R2.fq.gz so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R1.fq.gz fastq fastq 20557799368.0 101771284.0 E MTAB 13228:so zf94 VW5 MDMF2 CD45hi mhc2dab MACA S59 R 0:101 1:101 A:5872430236;C:4635392917;G:4244261404;T:5805533335;N:181476 101 101     5872430236 4635392917 4244261404 5805533335 181476 ERX11197446 ERS16222831 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.48524 0.49426 0.30765 0.31318 0.87008 0.86918 0.60597 0.58678 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11819 11819 ERR11799083 ERX11197442 ERS16222827 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 1 SAMEA114237382 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237382|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 1|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 1 p Sample 1 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R2.fq.gz so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R1.fq.gz fastq fastq 24592452226.0 121744813.0 E MTAB 13228:so zf94 VW1 P2Y12 CD45lo MGA S55 R 0:101 1:101 A:6964719283;C:5587681189;G:5075783189;T:6964040906;N:227659 101 101     6964719283 5587681189 5075783189 6964040906 227659 ERX11197442 ERS16222827 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.82038 0.82668 0.39096 0.39605 0.82532 0.82446 0.63514 0.57014 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11820 11820 ERR11799084 ERX11197443 ERS16222828 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 2 SAMEA114237383 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237383|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 2|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 2|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 2 p Sample 2 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R2.fq.gz so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R1.fq.gz fastq fastq 23692841994.0 117291297.0 E MTAB 13228:so zf94 VW2 P2Y12 CD45lo MGA S56 R 0:101 1:101 A:6997658831;C:5103576511;G:4615471075;T:6975924499;N:211078 101 101     6997658831 5103576511 4615471075 6975924499 211078 ERX11197443 ERS16222828 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.78961 0.79279 0.39456 0.39476 0.8227 0.82309 0.62072 0.61776 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
26484 26484 SRR26034368 SRX21751589 SRS18859096 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X9 tp53mut control GSM7774465   source name:brain|tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant|geo loc name:missing|collection date:missing 19521X9 tp53mut control The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant GSM7774465 GSM7774465: 19521X9 tp53mut control; Danio rerio; RNA Seq GSM7774465 r1 GSM7774465 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X9_220211_A00421_0418_AHGVTMDSX3_S180_L003_R2_001.fastq.gz 19521X9_220211_A00421_0418_AHGVTMDSX3_S180_L003_R1_001.fastq.gz fastq fastq 13111362918.0 43415109.0 GSM7774465 r1 0:151 1:151 A:3716297698;C:2842682328;G:2964203082;T:3588045151;N:134659 151 151     3716297698 2842682328 2964203082 3588045151 134659 SRX21751589 SRS18859096 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.87652 0.87774 0.39216 0.39133 0.71102 0.71133 0.53264 0.53118 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Adult Adult Brain Nervous System
26485 26485 SRR26034369 SRX21751588 SRS18859094 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X8 tp53mut control GSM7774464   source name:brain|tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant|geo loc name:missing|collection date:missing 19521X8 tp53mut control The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant GSM7774464 GSM7774464: 19521X8 tp53mut control; Danio rerio; RNA Seq GSM7774464 r1 GSM7774464 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X8_220211_A00421_0418_AHGVTMDSX3_S179_L003_R1_001.fastq.gz 19521X8_220211_A00421_0418_AHGVTMDSX3_S179_L003_R2_001.fastq.gz fastq fastq 13892147074.0 46000487.0 GSM7774464 r1 0:151 1:151 A:3814725425;C:3130415629;G:3297762528;T:3649099178;N:144314 151 151     3814725425 3130415629 3297762528 3649099178 144314 SRX21751588 SRS18859094 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.89624 0.89685 0.34529 0.34496 0.70092 0.70335 0.53129 0.53612 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Adult Adult Brain Nervous System
26486 26486 SRR26034370 SRX21751587 SRS18859095 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X7 tp53mut control GSM7774463   source name:brain|tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant|geo loc name:missing|collection date:missing 19521X7 tp53mut control The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant GSM7774463 GSM7774463: 19521X7 tp53mut control; Danio rerio; RNA Seq GSM7774463 r1 GSM7774463 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X7_220211_A00421_0418_AHGVTMDSX3_S178_L003_R1_001.fastq.gz 19521X7_220211_A00421_0418_AHGVTMDSX3_S178_L003_R2_001.fastq.gz fastq fastq 15619675560.0 51720780.0 GSM7774463 r1 0:151 1:151 A:4385995044;C:3423475528;G:3608910971;T:4201133585;N:160432 151 151     4385995044 3423475528 3608910971 4201133585 160432 SRX21751587 SRS18859095 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.88198 0.88184 0.36824 0.36836 0.70138 0.70427 0.50325 0.50812 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Adult Adult Brain Nervous System
26487 26487 SRR26034371 SRX21751586 SRS18859093 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X6 tp53het tumor GSM7774462   source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing 19521X6 tp53het tumor The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous GSM7774462 GSM7774462: 19521X6 tp53het tumor; Danio rerio; RNA Seq GSM7774462 r1 GSM7774462 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R1_001.fastq.gz 19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R2_001.fastq.gz fastq fastq 13856710696.0 45883148.0 GSM7774462 r1 0:151 1:151 A:3910050404;C:3019565763;G:3183961340;T:3742992264;N:140925 151 151     3910050404 3019565763 3183961340 3742992264 140925 SRX21751586 SRS18859093 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.8794 0.87909 0.38495 0.38479 0.69753 0.70005 0.49322 0.49442 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Juvenile Juvenile Brain Nervous System
26488 26488 SRR26034372 SRX21751585 SRS18859092 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X5 tp53het tumor GSM7774461   source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing 19521X5 tp53het tumor The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous GSM7774461 GSM7774461: 19521X5 tp53het tumor; Danio rerio; RNA Seq GSM7774461 r1 GSM7774461 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R1_001.fastq.gz 19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R2_001.fastq.gz fastq fastq 18644081740.0 61735370.0 GSM7774461 r1 0:151 1:151 A:5198614433;C:4108657498;G:4307546758;T:5029072002;N:191049 151 151     5198614433 4108657498 4307546758 5029072002 191049 SRX21751585 SRS18859092 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.88544 0.88842 0.35896 0.35863 0.69193 0.69248 0.49682 0.50274 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Juvenile Juvenile Brain Nervous System
26489 26489 SRR26034373 SRX21751584 SRS18859091 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X4 tp53het tumor GSM7774460   source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing 19521X4 tp53het tumor The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous GSM7774460 GSM7774460: 19521X4 tp53het tumor; Danio rerio; RNA Seq GSM7774460 r1 GSM7774460 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R1_001.fastq.gz 19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R2_001.fastq.gz fastq fastq 14417628886.0 47740493.0 GSM7774460 r1 0:151 1:151 A:4016299076;C:3183962020;G:3341158152;T:3876059438;N:150200 151 151     4016299076 3183962020 3341158152 3876059438 150200 SRX21751584 SRS18859091 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.89118 0.89184 0.33812 0.33641 0.68947 0.68954 0.49867 0.50026 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Juvenile Juvenile Brain Nervous System
26490 26490 SRR26034374 SRX21751583 SRS18859090 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X3 tp53mut tumor GSM7774459   source name:brain|tissue:brain|tumor status:tumor|age:4 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing 19521X3 tp53mut tumor The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:tumor|age:4 wpf|genotype:tp53 mutant GSM7774459 GSM7774459: 19521X3 tp53mut tumor; Danio rerio; RNA Seq GSM7774459 r1 GSM7774459 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X3_220211_A00421_0418_AHGVTMDSX3_S174_L003_R1_001.fastq.gz 19521X3_220211_A00421_0418_AHGVTMDSX3_S174_L003_R2_001.fastq.gz fastq fastq 14792155696.0 48980648.0 GSM7774459 r1 0:151 1:151 A:4164614124;C:3233958816;G:3393302319;T:4000129008;N:151429 151 151     4164614124 3233958816 3393302319 4000129008 151429 SRX21751583 SRS18859090 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.89303 0.8944 0.32883 0.32864 0.68024 0.68091 0.48335 0.48739 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Larval Larval Brain Nervous System
26491 26491 SRR26034375 SRX21751582 SRS18859089 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X2 tp53mut tumor GSM7774458   source name:brain|tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing 19521X2 tp53mut tumor The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant GSM7774458 GSM7774458: 19521X2 tp53mut tumor; Danio rerio; RNA Seq GSM7774458 r1 GSM7774458 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R1_001.fastq.gz 19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R2_001.fastq.gz fastq fastq 14064076580.0 46569790.0 GSM7774458 r1 0:151 1:151 A:3935649548;C:3089754695;G:3257286821;T:3781242542;N:142974 151 151     3935649548 3089754695 3257286821 3781242542 142974 SRX21751582 SRS18859089 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.89595 0.89655 0.35454 0.35431 0.68927 0.69077 0.47888 0.47831 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Juvenile Juvenile Brain Nervous System
26492 26492 SRR26034376 SRX21751581 SRS18859088 SRP459779 PRJNA1015242 Gene expression data from zebrafish SHH medulloblastoma brains and normal brains. GSE242897 Transcriptome Analysis Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.   pubmed:39078737   19521X1 tp53mut tumor GSM7774457   source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing 19521X1 tp53mut tumor The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts. brain Brains were frozen at 80C in RNA stabilization solution QIAGEN. Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598. Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee. tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant GSM7774457 GSM7774457: 19521X1 tp53mut tumor; Danio rerio; RNA Seq GSM7774457 r1 GSM7774457 1 Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP459779   loader:fastq load.py 19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R1_001.fastq.gz 19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R2_001.fastq.gz fastq fastq 16911500190.0 55998345.0 GSM7774457 r1 0:151 1:151 A:4750241986;C:3698380612;G:3890633834;T:4572071732;N:172026 151 151     4750241986 3698380612 3890633834 4572071732 172026 SRX21751581 SRS18859088 SRA1710210 Huntsman Cancer Institute Oncological Sciences, University of Utah 2 0.89695 0.89831 0.3562 0.35542 0.68392 0.68369 0.48172 0.48641 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United States 2023-09-11 Juvenile Juvenile Brain Nervous System
53495 53495 SRR9886611 SRX6639067 SRS5209782 SRP217245 PRJNA558074 Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings GSE135271 Transcriptome Analysis RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000   pubmed:32859696   GH6 GSM4002525   source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1 / GH6 A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample Brain   Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.   strain:LWT|tissue:Brain|age:12 wpf dj 1 / GSM4002525 GSM4002525: GH6; Danio rerio; RNA Seq GSM4002525   1 Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions. GEO Accession:GSM4002525 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP217245     GH6_S41_L004_R1_001.fastq-004.gz GH6_S41_L004_R2_001.fastq-009.gz fastq fastq 16197223984.0 53633192.0 GSM4002525 r1 0:151 1:151 A:4524520245;C:3580881754;G:3728671047;T:4362276906;N:874032 151 151     4524520245 3580881754 3728671047 4362276906 874032 SRX6639067 SRS5209782 SRA931013 GEO Biology, University of York 2 0.91745 0.9163 0.15171 0.14974 0.69826 0.70161 0.49509 0.48979 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United Kingdom 2019-08-01 Juvenile Juvenile Brain Nervous System
53496 53496 SRR9886610 SRX6639066 SRS5209781 SRP217245 PRJNA558074 Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings GSE135271 Transcriptome Analysis RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000   pubmed:32859696   GH5 GSM4002524   source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1 / GH5 A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample Brain   Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.   strain:LWT|tissue:Brain|age:12 wpf dj 1 / GSM4002524 GSM4002524: GH5; Danio rerio; RNA Seq GSM4002524   1 Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions. GEO Accession:GSM4002524 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP217245     GH5_S40_L004_R1_001.fastq-001.gz GH5_S40_L004_R2_001.fastq-003.gz fastq fastq 14762621304.0 48882852.0 GSM4002524 r1 0:151 1:151 A:4134788753;C:3245817056;G:3388258601;T:3992937107;N:819787 151 151     4134788753 3245817056 3388258601 3992937107 819787 SRX6639066 SRS5209781 SRA931013 GEO Biology, University of York 2 0.91356 0.91354 0.15637 0.15448 0.69755 0.70177 0.48873 0.49642 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United Kingdom 2019-08-01 Juvenile Juvenile Brain Nervous System
53497 53497 SRR9886609 SRX6639065 SRS5209780 SRP217245 PRJNA558074 Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings GSE135271 Transcriptome Analysis RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000   pubmed:32859696   GH4 GSM4002523   source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1 / GH4 A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample Brain   Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.   strain:LWT|tissue:Brain|age:12 wpf dj 1 / GSM4002523 GSM4002523: GH4; Danio rerio; RNA Seq GSM4002523   1 Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions. GEO Accession:GSM4002523 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP217245     GH4_S39_L004_R1_001.fastq-008.gz GH4_S39_L004_R2_001.fastq-011.gz fastq fastq 17232418376.0 57060988.0 GSM4002523 r1 0:151 1:151 A:4798343141;C:3812370940;G:3947002545;T:4673748329;N:953421 151 151     4798343141 3812370940 3947002545 4673748329 953421 SRX6639065 SRS5209780 SRA931013 GEO Biology, University of York 2 0.91359 0.91289 0.15791 0.15599 0.70128 0.70585 0.48423 0.48897 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United Kingdom 2019-08-01 Juvenile Juvenile Brain Nervous System
53498 53498 SRR9886608 SRX6639064 SRS5209779 SRP217245 PRJNA558074 Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings GSE135271 Transcriptome Analysis RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000   pubmed:32859696   GH3 GSM4002522   source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type GH3 A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample Brain   Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.   strain:LWT|tissue:Brain|age:12 wpf type GSM4002522 GSM4002522: GH3; Danio rerio; RNA Seq GSM4002522   1 Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions. GEO Accession:GSM4002522 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP217245     GH3_S38_L004_R1_001.fastq-002.gz GH3_S38_L004_R2_001.fastq-005.gz fastq fastq 15880659430.0 52584965.0 GSM4002522 r1 0:151 1:151 A:4428460730;C:3500855291;G:3647161094;T:4303300463;N:881852 151 151     4428460730 3500855291 3647161094 4303300463 881852 SRX6639064 SRS5209779 SRA931013 GEO Biology, University of York 2 0.91311 0.91404 0.15734 0.15592 0.69621 0.70092 0.4936 0.48217 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United Kingdom 2019-08-01 Juvenile Juvenile Brain Nervous System
53499 53499 SRR9886607 SRX6639063 SRS5209778 SRP217245 PRJNA558074 Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings GSE135271 Transcriptome Analysis RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000   pubmed:32859696   GH2 GSM4002521   source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type GH2 A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample Brain   Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.   strain:LWT|tissue:Brain|age:12 wpf type GSM4002521 GSM4002521: GH2; Danio rerio; RNA Seq GSM4002521   1 Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions. GEO Accession:GSM4002521 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP217245     GH2_S37_L004_R1_001.fastq-006.gz GH2_S37_L004_R2_001.fastq-012.gz fastq fastq 17721573816.0 58680708.0 GSM4002521 r1 0:151 1:151 A:4948184152;C:3901958410;G:4066182263;T:4804260891;N:988100 151 151     4948184152 3901958410 4066182263 4804260891 988100 SRX6639063 SRS5209778 SRA931013 GEO Biology, University of York 2 0.90975 0.90966 0.16242 0.16044 0.69934 0.70339 0.48497 0.49335 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United Kingdom 2019-08-01 Juvenile Juvenile Brain Nervous System
53500 53500 SRR9886606 SRX6639062 SRS5209777 SRP217245 PRJNA558074 Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings GSE135271 Transcriptome Analysis RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000   pubmed:32859696   GH1 GSM4002520   source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type GH1 A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample Brain   Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.   strain:LWT|tissue:Brain|age:12 wpf type GSM4002520 GSM4002520: GH1; Danio rerio; RNA Seq GSM4002520   1 Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions. GEO Accession:GSM4002520 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP217245     GH1_S36_L004_R1_001.fastq-007.gz GH1_S36_L004_R2_001.fastq-010.gz fastq fastq 16852076254.0 55801577.0 GSM4002520 r1 0:151 1:151 A:4697089825;C:3744087924;G:3878965083;T:4531030410;N:903012 151 151     4697089825 3744087924 3878965083 4531030410 903012 SRX6639062 SRS5209777 SRA931013 GEO Biology, University of York 2 0.91719 0.91765 0.15136 0.15011 0.69998 0.70455 0.48284 0.48335 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United Kingdom 2019-08-01 Juvenile Juvenile Brain Nervous System
68382 68382 SRR17720609 SRX13883476 SRS11752245 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m7G Normoxia IP GSM5832287   source name:zebrafish brain tissue|tissue:brain m7G Normoxia IP Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832287 GSM5832287: m7G Normoxia IP; Danio rerio; OTHER GSM5832287 r1 GSM5832287 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m7G_Normoxia_IP_R1.fastq.gz m7G_Normoxia_IP_R2.fastq.gz fastq fastq 6634104000.0 22113680.0 GSM5832287 r1 0:150 1:150 A:1396464650;C:1688319426;G:2250091870;T:1299109891;N:118163 150 150     1396464650 1688319426 2250091870 1299109891 118163 SRX13883476 SRS11752245 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.9266 0.92801 0.07275 0.06866 0.89964 0.90601 0.65995 0.75535 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68383 68383 SRR17720610 SRX13883475 SRS11752244 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m7G Normoxia Input GSM5832286   source name:zebrafish brain tissue|tissue:brain m7G Normoxia Input Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832286 GSM5832286: m7G Normoxia Input; Danio rerio; OTHER GSM5832286 r1 GSM5832286 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m7G_Normoxia_Input_R1.fastq.gz m7G_Normoxia_Input_R2.fastq.gz fastq fastq 6839977800.0 22799926.0 GSM5832286 r1 0:150 1:150 A:1986780958;C:1411210049;G:1509902094;T:1932043482;N:41217 150 150     1986780958 1411210049 1509902094 1932043482 41217 SRX13883475 SRS11752244 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.89709 0.89888 0.21747 0.21725 0.70021 0.69936 0.50469 0.51865 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68384 68384 SRR17720611 SRX13883474 SRS11752243 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m7G Hypoxia IP GSM5832285   source name:zebrafish brain tissue|tissue:brain m7G Hypoxia IP Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832285 GSM5832285: m7G Hypoxia IP; Danio rerio; OTHER GSM5832285 r1 GSM5832285 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m7G_Hypoxia_IP_R1.fastq.gz m7G_Hypoxia_IP_R2.fastq.gz fastq fastq 7282575000.0 24275250.0 GSM5832285 r1 0:150 1:150 A:1512757767;C:1913587260;G:2472336371;T:1383764924;N:128678 150 150     1512757767 1913587260 2472336371 1383764924 128678 SRX13883474 SRS11752243 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.94526 0.9467 0.05248 0.05071 0.91946 0.91981 0.69303 0.78448 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68385 68385 SRR17720612 SRX13883473 SRS11752241 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m7G Hypoxia Input GSM5832284   source name:zebrafish brain tissue|tissue:brain m7G Hypoxia Input Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832284 GSM5832284: m7G Hypoxia Input; Danio rerio; OTHER GSM5832284 r1 GSM5832284 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m7G_Hypoxia_Input_R1.fastq.gz m7G_Hypoxia_Input_R2.fastq.gz fastq fastq 7492311600.0 24974372.0 GSM5832284 r1 0:150 1:150 A:2208863421;C:1521950436;G:1608371217;T:2153082842;N:43684 150 150     2208863421 1521950436 1608371217 2153082842 43684 SRX13883473 SRS11752241 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.89264 0.89479 0.23239 0.23163 0.70496 0.70311 0.51741 0.52135 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68386 68386 SRR17720613 SRX13883472 SRS11752242 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m6A Normoxia IP GSM5832283   source name:zebrafish brain tissue|tissue:brain m6A Normoxia IP Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832283 GSM5832283: m6A Normoxia IP; Danio rerio; OTHER GSM5832283 r1 GSM5832283 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476     m6A_Normoxia_IP_R1.fastq.gz m6A_Normoxia_IP_R2.fastq.gz fastq fastq 6583667700.0 21945559.0 GSM5832283 r1 0:150 1:150 A:1750230540;C:1500991424;G:1592129260;T:1740287575;N:28901 150 150     1750230540 1500991424 1592129260 1740287575 28901 SRX13883472 SRS11752242 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.87682 0.87986 0.18203 0.17239 0.74671 0.7472 0.55638 0.55861 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68387 68387 SRR17720614 SRX13883471 SRS11752240 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m6A Normoxia Input GSM5832282   source name:zebrafish brain tissue|tissue:brain m6A Normoxia Input Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832282 GSM5832282: m6A Normoxia Input; Danio rerio; OTHER GSM5832282 r1 GSM5832282 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m6A_Normoxia_Input_R1.fastq.gz m6A_Normoxia_Input_R2.fastq.gz fastq fastq 6314076000.0 21046920.0 GSM5832282 r1 0:150 1:150 A:1815907910;C:1329572814;G:1378464668;T:1790102301;N:28307 150 150     1815907910 1329572814 1378464668 1790102301 28307 SRX13883471 SRS11752240 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.91754 0.91835 0.21273 0.20993 0.69702 0.69625 0.53456 0.53763 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68388 68388 SRR17720615 SRX13883470 SRS11752239 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m6A Hypoxia IP GSM5832281   source name:zebrafish brain tissue|tissue:brain m6A Hypoxia IP Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832281 GSM5832281: m6A Hypoxia IP; Danio rerio; OTHER GSM5832281 r1 GSM5832281 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476     m6A_Hypoxia_IP_R1.fastq.gz m6A_Hypoxia_IP_R2.fastq.gz fastq fastq 6490349100.0 21634497.0 GSM5832281 r1 0:150 1:150 A:1714144102;C:1483635762;G:1606044832;T:1686496024;N:28380 150 150     1714144102 1483635762 1606044832 1686496024 28380 SRX13883470 SRS11752239 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.87598 0.88161 0.16783 0.16105 0.74588 0.74568 0.55361 0.55307 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68389 68389 SRR17720616 SRX13883469 SRS11752237 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m6A Hypoxia Input GSM5832280   source name:zebrafish brain tissue|tissue:brain m6A Hypoxia Input Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832280 GSM5832280: m6A Hypoxia Input; Danio rerio; OTHER GSM5832280 r1 GSM5832280 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m6A_Hypoxia_Input_R1.fastq.gz m6A_Hypoxia_Input_R2.fastq.gz fastq fastq 7054483800.0 23514946.0 GSM5832280 r1 0:150 1:150 A:2000164754;C:1513377207;G:1570441784;T:1970468107;N:31948 150 150     2000164754 1513377207 1570441784 1970468107 31948 SRX13883469 SRS11752237 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.91916 0.91997 0.21403 0.21158 0.69716 0.69503 0.52616 0.51982 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68390 68390 SRR17720617 SRX13883468 SRS11752238 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m5C Normoxia IP GSM5832279   source name:zebrafish brain tissue|tissue:brain m5C Normoxia IP Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832279 GSM5832279: m5C Normoxia IP; Danio rerio; OTHER GSM5832279 r1 GSM5832279 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m5C_Normoxia_IP_R1.fastq.gz m5C_Normoxia_IP_R2.fastq.gz fastq fastq 7385723100.0 24619077.0 GSM5832279 r1 0:150 1:150 A:1779838658;C:1853060139;G:2010257354;T:1742536078;N:30871 150 150     1779838658 1853060139 2010257354 1742536078 30871 SRX13883468 SRS11752238 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.88617 0.87633 0.42619 0.41974 0.71792 0.74016 0.69827 0.68649 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68391 68391 SRR17720618 SRX13883467 SRS11752236 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m5C Normoxia Input GSM5832278   source name:zebrafish brain tissue|tissue:brain m5C Normoxia Input Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832278 GSM5832278: m5C Normoxia Input; Danio rerio; OTHER GSM5832278 r1 GSM5832278 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m5C_Normoxia_Input_R1.fastq.gz m5C_Normoxia_Input_R2.fastq.gz fastq fastq 6594811500.0 21982705.0 GSM5832278 r1 0:150 1:150 A:1941068575;C:1341378672;G:1414823713;T:1897501503;N:39037 150 150     1941068575 1341378672 1414823713 1897501503 39037 SRX13883467 SRS11752236 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.89423 0.89602 0.22595 0.2243 0.70212 0.70112 0.52954 0.52253 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68392 68392 SRR17720619 SRX13883466 SRS11752235 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m5C Hypoxia IP GSM5832277   source name:zebrafish brain tissue|tissue:brain m5C Hypoxia IP Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832277 GSM5832277: m5C Hypoxia IP; Danio rerio; OTHER GSM5832277 r1 GSM5832277 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m5C_Hypoxia_IP_R1.fastq.gz m5C_Hypoxia_IP_R2.fastq.gz fastq fastq 7837067100.0 26123557.0 GSM5832277 r1 0:150 1:150 A:1881167242;C:1973697370;G:2143523979;T:1838645554;N:32955 150 150     1881167242 1973697370 2143523979 1838645554 32955 SRX13883466 SRS11752235 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.87593 0.87108 0.45438 0.45093 0.71664 0.7321 0.67861 0.69742 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68393 68393 SRR17720620 SRX13883465 SRS11752233 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m5C Hypoxia Input GSM5832276   source name:zebrafish brain tissue|tissue:brain m5C Hypoxia Input Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832276 GSM5832276: m5C Hypoxia Input; Danio rerio; OTHER GSM5832276 r1 GSM5832276 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m5C_Hypoxia_Input_R1.fastq.gz m5C_Hypoxia_Input_R2.fastq.gz fastq fastq 8696183100.0 28987277.0 GSM5832276 r1 0:150 1:150 A:2564166903;C:1771446935;G:1858965930;T:2501551942;N:51390 150 150     2564166903 1771446935 1858965930 2501551942 51390 SRX13883465 SRS11752233 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.89379 0.89585 0.23898 0.23828 0.70272 0.70278 0.52965 0.50047 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68394 68394 SRR17720621 SRX13883464 SRS11752234 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m1A Normoxia IP GSM5832275   source name:zebrafish brain tissue|tissue:brain m1A Normoxia IP Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832275 GSM5832275: m1A Normoxia IP; Danio rerio; OTHER GSM5832275 r1 GSM5832275 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m1A_Normoxia_IP_R1.fastq.gz m1A_Normoxia_IP_R2.fastq.gz fastq fastq 6882734400.0 22942448.0 GSM5832275 r1 0:150 1:150 A:1321946139;C:1977632664;G:2310916241;T:1272200359;N:38997 150 150     1321946139 1977632664 2310916241 1272200359 38997 SRX13883464 SRS11752234 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.88367 0.88951 0.09774 0.09525 0.86395 0.86401 0.70125 0.74894 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68395 68395 SRR17720622 SRX13883463 SRS11752232 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m1A Normoxia Input GSM5832274   source name:zebrafish brain tissue|tissue:brain m1A Normoxia Input Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832274 GSM5832274: m1A Normoxia Input; Danio rerio; OTHER GSM5832274 r1 GSM5832274 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m1A_Normoxia_Input_R1.fastq.gz m1A_Normoxia_Input_R2.fastq.gz fastq fastq 7374452700.0 24581509.0 GSM5832274 r1 0:150 1:150 A:1511389847;C:2082118937;G:2325922232;T:1454979400;N:42284 150 150     1511389847 2082118937 2325922232 1454979400 42284 SRX13883463 SRS11752232 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.94589 0.94385 0.18226 0.18222 0.80878 0.8102 0.73686 0.71921 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68396 68396 SRR17720623 SRX13883462 SRS11752231 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m1A Hypoxia IP GSM5832273   source name:zebrafish brain tissue|tissue:brain m1A Hypoxia IP Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832273 GSM5832273: m1A Hypoxia IP; Danio rerio; OTHER GSM5832273 r1 GSM5832273 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m1A_Hypoxia_IP_R1.fastq.gz m1A_Hypoxia_IP_R2.fastq.gz fastq fastq 4861573800.0 16205246.0 GSM5832273 r1 0:150 1:150 A:927063480;C:1355342107;G:1698345464;T:880801957;N:20792 150 150     927063480 1355342107 1698345464 880801957 20792 SRX13883462 SRS11752231 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.8575 0.86165 0.10013 0.09909 0.87249 0.87221 0.72225 0.66629 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68397 68397 SRR17720624 SRX13883461 SRS11752229 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   m1A Hypoxia Input GSM5832272   source name:zebrafish brain tissue|tissue:brain m1A Hypoxia Input Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832272 GSM5832272: m1A Hypoxia Input; Danio rerio; OTHER GSM5832272 r1 GSM5832272 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py m1A_Hypoxia_Input_R1.fastq.gz m1A_Hypoxia_Input_R2.fastq.gz fastq fastq 7262130600.0 24207102.0 GSM5832272 r1 0:150 1:150 A:1553326396;C:2003023914;G:2214285414;T:1491453374;N:41502 150 150     1553326396 2003023914 2214285414 1491453374 41502 SRX13883461 SRS11752229 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.94247 0.94013 0.20625 0.20507 0.80188 0.80137 0.70188 0.73891 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68398 68398 SRR17720625 SRX13883460 SRS11752230 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   mRNA Normoxia GSM5832271   source name:zebrafish brain tissue|tissue:brain mRNA Normoxia Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832271 GSM5832271: mRNA Normoxia; Danio rerio; RNA Seq GSM5832271 r1 GSM5832271 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py mRNA_Normoxia_R1.fastq.gz mRNA_Normoxia_R2.fastq.gz fastq fastq 5600123100.0 18667077.0 GSM5832271 r1 0:150 1:150 A:1581506491;C:1211015791;G:1232941851;T:1574629930;N:29037 150 150     1581506491 1211015791 1232941851 1574629930 29037 SRX13883460 SRS11752230 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.88183 0.88417 0.48505 0.47939 0.71914 0.71867 0.49613 0.50205 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
68399 68399 SRR17720626 SRX13883459 SRS11752228 SRP356476 PRJNA800053 Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq GSE194284 Other The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …   pubmed:35135476   mRNA Hypoxia GSM5832270   source name:zebrafish brain tissue|tissue:brain mRNA Hypoxia Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites zebrafish brain tissue Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen. Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   tissue:brain GSM5832270 GSM5832270: mRNA Hypoxia; Danio rerio; RNA Seq GSM5832270 r1 GSM5832270 1 Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP356476   loader:fastq load.py mRNA_Hypoxia_R1.fastq.gz mRNA_Hypoxia_R2.fastq.gz fastq fastq 5576898600.0 18589662.0 GSM5832270 r1 0:150 1:150 A:1567886841;C:1214001571;G:1233723295;T:1561258221;N:28672 150 150     1567886841 1214001571 1233723295 1561258221 28672 SRX13883459 SRS11752228 SRA1361294 Affiliated Hospital of Guangdong Medical University Affiliated Hospital of Guangdong Medical University 2 0.88472 0.88798 0.46504 0.45892 0.72005 0.71752 0.49715 0.51843 150 150 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion nebnext bulk bulk bulk   China 2022-01-24 Adult Adult Brain Nervous System
70159 70159 SRR19560554 SRX15612628 SRS13313406 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a WT4 GSM6215039   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT dyrk1a WT4 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT GSM6215039 GSM6215039: dyrk1a WT4; Danio rerio; RNA Seq GSM6215039 r1 GSM6215039 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_WT4_055_138_S10_L001_R1_001.fastq.gz dyrk1a_WT4_055_138_S10_L001_R2_001.fastq.gz fastq fastq 7902803378.0 39122789.0 GSM6215039 r1 0:101 1:101 A:2306156032;C:1634172814;G:1752044587;T:2210254720;N:175225 101 101     2306156032 1634172814 1752044587 2210254720 175225 SRX15612628 SRS13313406 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.89674 0.89785 0.11283 0.1133 0.69455 0.69355 0.4786 0.47508 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70160 70160 SRR19560555 SRX15612627 SRS13313405 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a WT2 GSM6215038   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT dyrk1a WT2 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT GSM6215038 GSM6215038: dyrk1a WT2; Danio rerio; RNA Seq GSM6215038 r1 GSM6215038 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_WT2_067_126_S9_L001_R1_001.fastq.gz dyrk1a_WT2_067_126_S9_L001_R2_001.fastq.gz fastq fastq 7079496222.0 35047011.0 GSM6215038 r1 0:101 1:101 A:2065386157;C:1460884924;G:1579377775;T:1973689055;N:158311 101 101     2065386157 1460884924 1579377775 1973689055 158311 SRX15612627 SRS13313405 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.89733 0.89769 0.10808 0.1082 0.69473 0.69246 0.4714 0.46904 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70161 70161 SRR19560556 SRX15612626 SRS13313404 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a WT1 GSM6215037   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT dyrk1a WT1 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT GSM6215037 GSM6215037: dyrk1a WT1; Danio rerio; RNA Seq GSM6215037 r1 GSM6215037 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_WT1_079_114_S8_L001_R1_001.fastq.gz dyrk1a_WT1_079_114_S8_L001_R2_001.fastq.gz fastq fastq 6622132670.0 32782835.0 GSM6215037 r1 0:101 1:101 A:1948249689;C:1344786648;G:1444984183;T:1883963959;N:148191 101 101     1948249689 1344786648 1444984183 1883963959 148191 SRX15612626 SRS13313404 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.88644 0.8854 0.1325 0.13284 0.69745 0.69455 0.48645 0.48809 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70162 70162 SRR19560557 SRX15612625 SRS13313403 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a HET4 GSM6215036   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET dyrk1a HET4 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET GSM6215036 GSM6215036: dyrk1a HET4; Danio rerio; RNA Seq GSM6215036 r1 GSM6215036 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_Het4_091_102_S7_L001_R1_001.fastq.gz dyrk1a_Het4_091_102_S7_L001_R2_001.fastq.gz fastq fastq 6825687060.0 33790530.0 GSM6215036 r1 0:101 1:101 A:1996927388;C:1382413394;G:1491219728;T:1954975088;N:151462 101 101     1996927388 1382413394 1491219728 1954975088 151462 SRX15612625 SRS13313403 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.8771 0.87636 0.13953 0.13921 0.70134 0.70082 0.48309 0.49155 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70163 70163 SRR19560558 SRX15612624 SRS13313402 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a HET3 GSM6215035   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET dyrk1a HET3 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET GSM6215035 GSM6215035: dyrk1a HET3; Danio rerio; RNA Seq GSM6215035 r1 GSM6215035 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_Het3_008_185_S6_L001_R1_001.fastq.gz dyrk1a_Het3_008_185_S6_L001_R2_001.fastq.gz fastq fastq 9512968204.0 47093902.0 GSM6215035 r1 0:101 1:101 A:2793571739;C:1936475456;G:2088476685;T:2694233049;N:211275 101 101     2793571739 1936475456 2088476685 2694233049 211275 SRX15612624 SRS13313402 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.88305 0.88109 0.13901 0.13926 0.69856 0.69615 0.48988 0.48919 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70164 70164 SRR19560559 SRX15612623 SRS13313401 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a HET2 GSM6215034   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET dyrk1a HET2 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET GSM6215034 GSM6215034: dyrk1a HET2; Danio rerio; RNA Seq GSM6215034 r1 GSM6215034 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_Het2_020_173_S5_L001_R1_001.fastq.gz dyrk1a_Het2_020_173_S5_L001_R2_001.fastq.gz fastq fastq 7644875638.0 37845919.0 GSM6215034 r1 0:101 1:101 A:2190708434;C:1609961798;G:1719044598;T:2124991128;N:169680 101 101     2190708434 1609961798 1719044598 2124991128 169680 SRX15612623 SRS13313401 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.893 0.89318 0.07847 0.07861 0.69325 0.69191 0.4503 0.45105 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70165 70165 SRR19560560 SRX15612622 SRS13313400 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a HOM5 GSM6215033   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM dyrk1a HOM5 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM GSM6215033 GSM6215033: dyrk1a HOM5; Danio rerio; RNA Seq GSM6215033 r1 GSM6215033 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_Hom5_032_161_S4_L001_R1_001.fastq.gz dyrk1a_Hom5_032_161_S4_L001_R2_001.fastq.gz fastq fastq 6286655716.0 31122058.0 GSM6215033 r1 0:101 1:101 A:1884291009;C:1241960690;G:1345362712;T:1814899144;N:142161 101 101     1884291009 1241960690 1345362712 1814899144 142161 SRX15612622 SRS13313400 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.8708 0.87099 0.1837 0.18358 0.71346 0.71043 0.52327 0.52172 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70166 70166 SRR19560561 SRX15612621 SRS13313399 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a HOM3 GSM6215032   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM dyrk1a HOM3 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM GSM6215032 GSM6215032: dyrk1a HOM3; Danio rerio; RNA Seq GSM6215032 r1 GSM6215032 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_Hom3_044_149_S3_L001_R1_001.fastq.gz dyrk1a_Hom3_044_149_S3_L001_R2_001.fastq.gz fastq fastq 7148763840.0 35389920.0 GSM6215032 r1 0:101 1:101 A:2092747707;C:1464796550;G:1572724974;T:2018333200;N:161409 101 101     2092747707 1464796550 1572724974 2018333200 161409 SRX15612621 SRS13313399 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.88908 0.88682 0.13424 0.13371 0.69203 0.6913 0.49374 0.49311 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70167 70167 SRR19560562 SRX15612620 SRS13313398 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a HOM2 GSM6215031   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM dyrk1a HOM2 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM GSM6215031 GSM6215031: dyrk1a HOM2; Danio rerio; RNA Seq GSM6215031 r1 GSM6215031 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_Hom2_056_137_S2_L001_R1_001.fastq.gz dyrk1a_Hom2_056_137_S2_L001_R2_001.fastq.gz fastq fastq 5786861054.0 28647827.0 GSM6215031 r1 0:101 1:101 A:1671012970;C:1197032060;G:1296060748;T:1622623090;N:132186 101 101     1671012970 1197032060 1296060748 1622623090 132186 SRX15612620 SRS13313398 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.88887 0.88943 0.08816 0.08816 0.69262 0.68994 0.47509 0.47239 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70168 70168 SRR19560563 SRX15612619 SRS13313397 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   dyrk1a HOM1 GSM6215030   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM dyrk1a HOM1 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM GSM6215030 GSM6215030: dyrk1a HOM1; Danio rerio; RNA Seq GSM6215030 r1 GSM6215030 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py dyrk1a_Hom1_068_125_S1_L001_R1_001.fastq.gz dyrk1a_Hom1_068_125_S1_L001_R2_001.fastq.gz fastq fastq 6721969150.0 33277075.0 GSM6215030 r1 0:101 1:101 A:1943487755;C:1388497581;G:1509724133;T:1880112182;N:147499 101 101     1943487755 1388497581 1509724133 1880112182 147499 SRX15612619 SRS13313397 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.892 0.89258 0.08973 0.09 0.69804 0.69619 0.47477 0.47297 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70169 70169 SRR19560573 SRX15612609 SRS13313387 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab WT3 GSM6215020   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT scn1lab WT3 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT GSM6215020 GSM6215020: scn1lab WT3; Danio rerio; RNA Seq GSM6215020 r1 GSM6215020 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_WT3_R1.fastq.gz Dec8_scn1_WT3_R2.fastq.gz fastq fastq 8755553246.0 43344323.0 GSM6215020 r1 0:101 1:101 A:2522756407;C:1825383888;G:2009734783;T:2397482724;N:195444 101 101     2522756407 1825383888 2009734783 2397482724 195444 SRX15612609 SRS13313387 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.88631 0.89209 0.13849 0.13882 0.68359 0.68373 0.48499 0.48536 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70170 70170 SRR19560574 SRX15612608 SRS13313386 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab WT2 GSM6215019   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT scn1lab WT2 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT GSM6215019 GSM6215019: scn1lab WT2; Danio rerio; RNA Seq GSM6215019 r1 GSM6215019 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_WT2_R1.fastq.gz Dec8_scn1_WT2_R2.fastq.gz fastq fastq 9208034256.0 45584328.0 GSM6215019 r1 0:101 1:101 A:2708559207;C:1845326645;G:2043146078;T:2610799023;N:203303 101 101     2708559207 1845326645 2043146078 2610799023 203303 SRX15612608 SRS13313386 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.8783 0.88175 0.15498 0.15526 0.69031 0.68935 0.5029 0.50682 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70171 70171 SRR19560575 SRX15612607 SRS13313385 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab WT1 GSM6215018   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT scn1lab WT1 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT GSM6215018 GSM6215018: scn1lab WT1; Danio rerio; RNA Seq GSM6215018 r1 GSM6215018 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_WT1_R1.fastq.gz Dec8_scn1_WT1_R2.fastq.gz fastq fastq 8866777880.0 43894940.0 GSM6215018 r1 0:101 1:101 A:2619286212;C:1773731842;G:1954443989;T:2519120249;N:195588 101 101     2619286212 1773731842 1954443989 2519120249 195588 SRX15612607 SRS13313385 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.87792 0.87896 0.1645 0.16446 0.69873 0.69767 0.50758 0.50857 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70172 70172 SRR19560576 SRX15612606 SRS13313384 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab HET3 GSM6215017   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET scn1lab HET3 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET GSM6215017 GSM6215017: scn1lab HET3; Danio rerio; RNA Seq GSM6215017 r1 GSM6215017 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_HET3_R1.fastq.gz Dec8_scn1_HET3_R2.fastq.gz fastq fastq 9837485850.0 48700425.0 GSM6215017 r1 0:101 1:101 A:3058002601;C:1783589847;G:1999426374;T:2996247689;N:219339 101 101     3058002601 1783589847 1999426374 2996247689 219339 SRX15612606 SRS13313384 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.79228 0.79265 0.19829 0.19897 0.768 0.76881 0.63874 0.60993 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70173 70173 SRR19560577 SRX15612605 SRS13313383 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab HET2 GSM6215016   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET scn1lab HET2 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET GSM6215016 GSM6215016: scn1lab HET2; Danio rerio; RNA Seq GSM6215016 r1 GSM6215016 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_HET2_R1.fastq.gz Dec8_scn1_HET2_R2.fastq.gz fastq fastq 7904076382.0 39129091.0 GSM6215016 r1 0:101 1:101 A:2313856206;C:1597073570;G:1729185251;T:2263789669;N:171686 101 101     2313856206 1597073570 1729185251 2263789669 171686 SRX15612605 SRS13313383 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.87286 0.87498 0.13182 0.13228 0.72001 0.71989 0.54792 0.5451 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70174 70174 SRR19560578 SRX15612604 SRS13313381 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab HET1 GSM6215015   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET scn1lab HET1 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET GSM6215015 GSM6215015: scn1lab HET1; Danio rerio; RNA Seq GSM6215015 r1 GSM6215015 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_HET1_R1.fastq.gz Dec8_scn1_HET1_R2.fastq.gz fastq fastq 10583641934.0 52394267.0 GSM6215015 r1 0:101 1:101 A:3069468722;C:2179597536;G:2345048883;T:2989294494;N:232299 101 101     3069468722 2179597536 2345048883 2989294494 232299 SRX15612604 SRS13313381 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.87752 0.8777 0.12364 0.12313 0.71654 0.71737 0.48643 0.47848 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70175 70175 SRR19560579 SRX15612603 SRS13313382 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab HOM3 GSM6215014   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM scn1lab HOM3 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM GSM6215014 GSM6215014: scn1lab HOM3; Danio rerio; RNA Seq GSM6215014 r1 GSM6215014 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_HOM3_R1.fastq.gz Dec8_scn1_HOM3_R2.fastq.gz fastq fastq 7777420766.0 38502083.0 GSM6215014 r1 0:101 1:101 A:2213965945;C:1621764946;G:1767224135;T:2174292493;N:173247 101 101     2213965945 1621764946 1767224135 2174292493 173247 SRX15612603 SRS13313382 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.88412 0.88408 0.09074 0.09152 0.72338 0.72403 0.51741 0.51684 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70176 70176 SRR19560580 SRX15612602 SRS13313380 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab HOM2 GSM6215013   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM scn1lab HOM2 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM GSM6215013 GSM6215013: scn1lab HOM2; Danio rerio; RNA Seq GSM6215013 r1 GSM6215013 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_HOM2_R1.fastq.gz Dec8_scn1_HOM2_R2.fastq.gz fastq fastq 8568922820.0 42420410.0 GSM6215013 r1 0:101 1:101 A:2555761269;C:1697178868;G:1896122512;T:2419672664;N:187507 101 101     2555761269 1697178868 1896122512 2419672664 187507 SRX15612602 SRS13313380 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.87147 0.87346 0.14976 0.14929 0.70571 0.70611 0.52591 0.52781 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70177 70177 SRR19560581 SRX15612601 SRS13313379 SRP378803 PRJNA846486 High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways GSE205578 Transcriptome Analysis Investigation of convergence and divergence of different Autism Risk genes at the molecular level in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.   pubmed:36933215   scn1lab HOM1 GSM6215012   source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM scn1lab HOM1 DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0 https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al. 2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al. 2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05 fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al. 2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample Whole Brain   Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM GSM6215012 GSM6215012: scn1lab HOM1; Danio rerio; RNA Seq GSM6215012 r1 GSM6215012 1 Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll RNA Isolation Kit Invitrogen. To control for background variation RNA was extracted from sibling or cousin matched larvae from heterozygous incrosses of scn1labΔ44/+ chd8Δ5/+ and dyrk1aaΔ77/+:dyrk1abΔ8/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP378803   loader:fastq load.py Dec8_scn1_HOM1_R1.fastq.gz Dec8_scn1_HOM1_R2.fastq.gz fastq fastq 7104138808.0 35169004.0 GSM6215012 r1 0:101 1:101 A:2086867330;C:1422921410;G:1555208321;T:2038985303;N:156444 101 101     2086867330 1422921410 1555208321 2038985303 156444 SRX15612601 SRS13313379 SRA1432967 Hoffman Lab, Neuroscience, Yale University Hoffman Lab, Neuroscience, Yale University 2 0.86112 0.86909 0.13235 0.13356 0.72143 0.72092 0.42339 0.43557 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2022-06-06 Larval Larval Brain Nervous System
70436 70436 SRR19846950 SRX15890625 SRS13579729 SRP383494 PRJNA852585 Control of cranial ectomesenchyme fate by Nr2f nuclear receptors GSE206903 Transcriptome Analysis Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.   pubmed:36367707   sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 2 GSM6266712   tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 2 Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript. sox10:DsRed+ neural crest cells   Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf GSM6266712 GSM6266712: sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 2; Danio rerio; RNA Seq GSM6266712 r1 GSM6266712 1 Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP383494   loader:fastq load.py sox10DsRed-CON2-S6-R1.fastq.gz sox10DsRed-CON2-S6_R2_001.fastq.gz fastq fastq 4876722704.0 32083702.0 GSM6266712 r1 0:76 1:76 A:1342673931;C:1107276249;G:1150211941;T:1276364234;N:196349 76 76     1342673931 1107276249 1150211941 1276364234 196349 SRX15890625 SRS13579729     Human Genetics, Cincinnati Children's Hospital Medical Center 2 0.8977 0.90038 0.03951 0.04044 0.75777 0.76331 0.46312 0.4722 76 76 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk bulk bulk   United States 2022-06-24 Segmentation Embryo Brain Nervous System
70437 70437 SRR19846951 SRX15890624 SRS13579728 SRP383494 PRJNA852585 Control of cranial ectomesenchyme fate by Nr2f nuclear receptors GSE206903 Transcriptome Analysis Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.   pubmed:36367707   sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 1 GSM6266711   tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 1 Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript. sox10:DsRed+ neural crest cells   Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf GSM6266711 GSM6266711: sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 1; Danio rerio; RNA Seq GSM6266711 r1 GSM6266711 1 Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP383494   loader:fastq load.py sox10DsRed-CON1-S5-R1.fastq.gz sox10DsRed-CON1-S5-R2.fastq.gz fastq fastq 4875797328.0 32077614.0 GSM6266711 r1 0:76 1:76 A:1340486054;C:1109815504;G:1153492417;T:1271807986;N:195367 76 76     1340486054 1109815504 1153492417 1271807986 195367 SRX15890624 SRS13579728     Human Genetics, Cincinnati Children's Hospital Medical Center 2 0.92525 0.92846 0.04508 0.04513 0.75789 0.76217 0.47713 0.47624 76 76 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk bulk bulk   United States 2022-06-24 Segmentation Embryo Brain Nervous System
70438 70438 SRR19846952 SRX15890623 SRS13579727 SRP383494 PRJNA852585 Control of cranial ectomesenchyme fate by Nr2f nuclear receptors GSE206903 Transcriptome Analysis Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.   pubmed:36367707   sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 2 GSM6266710   tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:nr2f2[unk]; nr2f5[mut]|developmental stage:20 hpf sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 2 Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript. sox10:DsRed+ neural crest cells   Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   cell type:sox10:DsRed+ neural crest cells|genotype:nr2f2[unk]; nr2f5[mut]|developmental stage:20 hpf GSM6266710 GSM6266710: sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 2; Danio rerio; RNA Seq GSM6266710 r1 GSM6266710 1 Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP383494   loader:fastq load.py sox10DsRed-MUT2-S2-R1.fastq.gz sox10DsRed-MUT2-S2-R2.fastq.gz fastq fastq 4289333904.0 28219302.0 GSM6266710 r1 0:76 1:76 A:1191429143;C:963361475;G:1000468087;T:1133905434;N:169765 76 76     1191429143 963361475 1000468087 1133905434 169765 SRX15890623 SRS13579727     Human Genetics, Cincinnati Children's Hospital Medical Center 2 0.8017 0.80251 0.0318 0.03187 0.78106 0.78606 0.46375 0.46931 76 76 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk bulk bulk   United States 2022-06-24 Segmentation Embryo Brain Nervous System
70439 70439 SRR19846953 SRX15890622 SRS13579726 SRP383494 PRJNA852585 Control of cranial ectomesenchyme fate by Nr2f nuclear receptors GSE206903 Transcriptome Analysis Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.   pubmed:36367707   sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1 GSM6266709   tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:nr2f2[unk]; nr2f5[mut]|developmental stage:20 hpf sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1 Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript. sox10:DsRed+ neural crest cells   Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   cell type:sox10:DsRed+ neural crest cells|genotype:nr2f2[unk]; nr2f5[mut]|developmental stage:20 hpf GSM6266709 GSM6266709: sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1; Danio rerio; RNA Seq GSM6266709 r1 GSM6266709 1 Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP383494   loader:fastq load.py sox10DsRed-MUT1-S1-R1.fastq.gz sox10DsRed-MUT1-S1_R2_001.fastq.gz fastq fastq 4812271816.0 31659683.0 GSM6266709 r1 0:76 1:76 A:1327161695;C:1091694077;G:1133722041;T:1259497189;N:196814 76 76     1327161695 1091694077 1133722041 1259497189 196814 SRX15890622 SRS13579726     Human Genetics, Cincinnati Children's Hospital Medical Center 2 0.90398 0.90573 0.03493 0.0351 0.76928 0.77429 0.46651 0.46743 76 76 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk bulk bulk   United States 2022-06-24 Segmentation Embryo Brain Nervous System
71453 71453 SRR21631156 SRX17631564 SRS15166367 SRP398129 PRJNA882122 Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish GSE213728 Transcriptome Analysis Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.       tNCCs treated 100uM cyclopamine Sample4 GSM6592894   source name:neural crest cells|tissue:neural crest cells|genotype:wildtype|treatment:100uM Cyclopamine 50%epiboly to 24hpf|geo loc name:missing|collection date:missing tNCCs treated 100uM cyclopamine Sample4 Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file neural crest cells For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf standard Illumina Kit for stranded RNAseq Embryos reared at 28C until 24hpf. tissue:neural crest cells|genotype:wildtype|treatment:100uM Cyclopamine 50%epiboly to 24hpf GSM6592894 GSM6592894: tNCCs treated 100uM cyclopamine Sample4; Danio rerio; RNA Seq GSM6592894 r1 GSM6592894 1 standard Illumina Kit for stranded RNAseq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP398129   loader:fastq load.py S1_100uM_RFP_S41_L001_R1_001.fastq.gz S1_100uM_RFP_S41_L001_R2_001.fastq.gz fastq fastq 13002170590.0 43053545.0 GSM6592894 r1 0:151 1:151 A:3161816467;C:2810101954;G:4085613729;T:2944516445;N:121995 151 151     3161816467 2810101954 4085613729 2944516445 121995 SRX17631564 SRS15166367 SRA1501497 Lencer Laboratory, Department of Biology, Lafayette College Lencer Laboratory, Department of Biology, Lafayette College 2 0.87647 0.86789 0.10005 0.09935 0.77439 0.77646 0.48741 0.49136 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2022-09-19 Multi-stage Embryo Brain Nervous System
71454 71454 SRR21631157 SRX17631563 SRS15166366 SRP398129 PRJNA882122 Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish GSE213728 Transcriptome Analysis Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.       tNCCs treated 100uM cyclopamine Sample3 GSM6592893   source name:neural crest cells|tissue:neural crest cells|genotype:wildtype|treatment:100uM Cyclopamine 50%epiboly to 24hpf|geo loc name:missing|collection date:missing tNCCs treated 100uM cyclopamine Sample3 Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file neural crest cells For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf standard Illumina Kit for stranded RNAseq Embryos reared at 28C until 24hpf. tissue:neural crest cells|genotype:wildtype|treatment:100uM Cyclopamine 50%epiboly to 24hpf GSM6592893 GSM6592893: tNCCs treated 100uM cyclopamine Sample3; Danio rerio; RNA Seq GSM6592893 r1 GSM6592893 1 standard Illumina Kit for stranded RNAseq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP398129   loader:fastq load.py Sample5_RFP_Cya_S5_L002_R1_001.fastq.gz Sample5_RFP_Cya_S5_L002_R2_001.fastq.gz fastq fastq 14670089410.0 48576455.0 GSM6592893 r1 0:151 1:151 A:3582551264;C:3258860261;G:4484646058;T:3341778251;N:2253576 151 151     3582551264 3258860261 4484646058 3341778251 2253576 SRX17631563 SRS15166366 SRA1501497 Lencer Laboratory, Department of Biology, Lafayette College Lencer Laboratory, Department of Biology, Lafayette College 2 0.88985 0.89469 0.09902 0.10014 0.75629 0.75745 0.5281 0.52768 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2022-09-19 Multi-stage Embryo Brain Nervous System
71455 71455 SRR21631158 SRX17631562 SRS15166365 SRP398129 PRJNA882122 Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish GSE213728 Transcriptome Analysis Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.       Slow twitch NCC tgsox10:mRFP Sample2 GSM6592892   source name:neural crest cells|tissue:neural crest cells|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing Slow twitch NCC tgsox10:mRFP Sample2 Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file neural crest cells For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf standard Illumina Kit for stranded RNAseq Embryos reared at 28C until 24hpf. tissue:neural crest cells|genotype:wildtype|treatment:n1 GSM6592892 GSM6592892: Slow twitch NCC tgsox10:mRFP Sample2; Danio rerio; RNA Seq GSM6592892 r1 GSM6592892 1 standard Illumina Kit for stranded RNAseq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP398129   loader:fastq load.py Sample4_RFP_24hpf_S4_L002_R1_001.fastq.gz Sample4_RFP_24hpf_S4_L002_R2_001.fastq.gz fastq fastq 13884740524.0 45975962.0 GSM6592892 r1 0:151 1:151 A:3031916247;C:2738677707;G:5291000892;T:2821006628;N:2139050 151 151     3031916247 2738677707 5291000892 2821006628 2139050 SRX17631562 SRS15166365 SRA1501497 Lencer Laboratory, Department of Biology, Lafayette College Lencer Laboratory, Department of Biology, Lafayette College 2 0.90321 0.87636 0.09526 0.09316 0.77674 0.77885 0.52923 0.52674 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2022-09-19 Pharyngula Embryo Brain Nervous System
71457 71457 SRR21631160 SRX17631560 SRS15166363 SRP398129 PRJNA882122 Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish GSE213728 Transcriptome Analysis Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.       Slow twitch NCC tgsox10:mRFP Sample1 GSM6592890   source name:neural crest cells|tissue:neural crest cells|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing Slow twitch NCC tgsox10:mRFP Sample1 Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file neural crest cells For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf standard Illumina Kit for stranded RNAseq Embryos reared at 28C until 24hpf. tissue:neural crest cells|genotype:wildtype|treatment:n1 GSM6592890 GSM6592890: Slow twitch NCC tgsox10:mRFP Sample1; Danio rerio; RNA Seq GSM6592890 r1 GSM6592890 1 standard Illumina Kit for stranded RNAseq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP398129   loader:fastq load.py Sample2_RFP_24hpf_S2_L002_R1_001.fastq.gz Sample2_RFP_24hpf_S2_L002_R2_001.fastq.gz fastq fastq 17922118728.0 59344764.0 GSM6592890 r1 0:151 1:151 A:3817111411;C:3344863596;G:7286590230;T:3470806637;N:2746854 151 151     3817111411 3344863596 7286590230 3470806637 2746854 SRX17631560 SRS15166363 SRA1501497 Lencer Laboratory, Department of Biology, Lafayette College Lencer Laboratory, Department of Biology, Lafayette College 2 0.90833 0.90047 0.10346 0.10249 0.78624 0.7878 0.53598 0.52984 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2022-09-19 Pharyngula Embryo Brain Nervous System
74621 74621 SRR23883665 SRX19695587 SRS17064513 SRP427757 PRJNA945489 Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency GSE227551 Transcriptome Analysis Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality. To investigate the mechanisms driving saposin loss associated demyelination the brains of psap / zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene which codes for saposins A D. Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing and fish carrying the mutations of interest were propagated to homozygosity. RNA was isolated from the brains of four mpf psap / zebrafish and wildtype siblings.   pubmed:37183607   Brain psap knockout 4 mpf replicate 4 [15628X8] GSM7102585   source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf Brain psap knockout 4 mpf replicate 4 [15628X8] Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34 reads were trimmed of adapters using cutadapt 1.16 alignment was performed with STAR two pass mode and genes were assigned using featureCounts version 1.6.3. Output files cutadapt FastQC Picard CollectRnaSeqMetrics STAR and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID and fold changes/adjusted p values annotated by gene name Brain 3 per sample   RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf GSM7102585 GSM7102585: Brain psap knockout 4 mpf replicate 4 [15628X8]; Danio rerio; RNA Seq GSM7102585 r1 GSM7102585 1 RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP427757   loader:fastq load.py psap4_R1.fastq.gz psap4_R2.fastq.gz fastq fastq 14570988714.0 48248307.0 GSM7102585 r1 0:151 1:151 A:4091189239;C:3187243752;G:3301025523;T:3991388289;N:141911 151 151     4091189239 3187243752 3301025523 3991388289 141911 SRX19695587 SRS17064513 SRA1606419 Peterson, Pharmacology and Toxicology, University of Utah Peterson, Pharmacology and Toxicology, University of Utah 2 0.90366 0.90563 0.345 0.34498 0.67801 0.67765 0.49732 0.49797 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion ribozero bulk bulk bulk   United States 2023-03-16 Adult Adult Brain Nervous System
74622 74622 SRR23883666 SRX19695586 SRS17064512 SRP427757 PRJNA945489 Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency GSE227551 Transcriptome Analysis Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality. To investigate the mechanisms driving saposin loss associated demyelination the brains of psap / zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene which codes for saposins A D. Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing and fish carrying the mutations of interest were propagated to homozygosity. RNA was isolated from the brains of four mpf psap / zebrafish and wildtype siblings.   pubmed:37183607   Brain wildtype 4 mpf replicate 4 [15628X7] GSM7102584   source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:wildtype|treatment:n1|time:4 mpf Brain wildtype 4 mpf replicate 4 [15628X7] Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34 reads were trimmed of adapters using cutadapt 1.16 alignment was performed with STAR two pass mode and genes were assigned using featureCounts version 1.6.3. Output files cutadapt FastQC Picard CollectRnaSeqMetrics STAR and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID and fold changes/adjusted p values annotated by gene name Brain 3 per sample   RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   tissue:Brain 3 per sample|strain:TuAB|genotype:wildtype|treatment:n1|time:4 mpf GSM7102584 GSM7102584: Brain wildtype 4 mpf replicate 4 [15628X7]; Danio rerio; RNA Seq GSM7102584 r1 GSM7102584 1 RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP427757   loader:fastq load.py WT4_R1.fastq.gz WT4_R2.fastq.gz fastq fastq 15735211096.0 52103348.0 GSM7102584 r1 0:151 1:151 A:4544021774;C:3315018583;G:3457222528;T:4418793663;N:154548 151 151     4544021774 3315018583 3457222528 4418793663 154548 SRX19695586 SRS17064512 SRA1606419 Peterson, Pharmacology and Toxicology, University of Utah Peterson, Pharmacology and Toxicology, University of Utah 2 0.88784 0.88776 0.42684 0.42573 0.70402 0.70469 0.49003 0.4875 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion ribozero bulk bulk bulk   United States 2023-03-16 Adult Adult Brain Nervous System
74623 74623 SRR23883667 SRX19695585 SRS17064511 SRP427757 PRJNA945489 Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency GSE227551 Transcriptome Analysis Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality. To investigate the mechanisms driving saposin loss associated demyelination the brains of psap / zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene which codes for saposins A D. Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing and fish carrying the mutations of interest were propagated to homozygosity. RNA was isolated from the brains of four mpf psap / zebrafish and wildtype siblings.   pubmed:37183607   Brain psap knockout 4 mpf replicate 3 [15628X6] GSM7102583   source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf Brain psap knockout 4 mpf replicate 3 [15628X6] Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34 reads were trimmed of adapters using cutadapt 1.16 alignment was performed with STAR two pass mode and genes were assigned using featureCounts version 1.6.3. Output files cutadapt FastQC Picard CollectRnaSeqMetrics STAR and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID and fold changes/adjusted p values annotated by gene name Brain 3 per sample   RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf GSM7102583 GSM7102583: Brain psap knockout 4 mpf replicate 3 [15628X6]; Danio rerio; RNA Seq GSM7102583 r1 GSM7102583 1 RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP427757   loader:fastq load.py psap3_R1.fastq.gz psap3_R2.fastq.gz fastq fastq 13975310928.0 46275864.0 GSM7102583 r1 0:151 1:151 A:3989858735;C:2982111603;G:3103138900;T:3900064634;N:137056 151 151     3989858735 2982111603 3103138900 3900064634 137056 SRX19695585 SRS17064511 SRA1606419 Peterson, Pharmacology and Toxicology, University of Utah Peterson, Pharmacology and Toxicology, University of Utah 2 0.89327 0.8944 0.41562 0.41551 0.68757 0.68793 0.50307 0.50423 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion ribozero bulk bulk bulk   United States 2023-03-16 Adult Adult Brain Nervous System
74624 74624 SRR23883668 SRX19695584 SRS17064510 SRP427757 PRJNA945489 Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency GSE227551 Transcriptome Analysis Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality. To investigate the mechanisms driving saposin loss associated demyelination the brains of psap / zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene which codes for saposins A D. Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing and fish carrying the mutations of interest were propagated to homozygosity. RNA was isolated from the brains of four mpf psap / zebrafish and wildtype siblings.   pubmed:37183607   Brain wildtype 4 mpf replicate 3 [15628X5] GSM7102582   source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:wildtype|treatment:n1|time:4 mpf Brain wildtype 4 mpf replicate 3 [15628X5] Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34 reads were trimmed of adapters using cutadapt 1.16 alignment was performed with STAR two pass mode and genes were assigned using featureCounts version 1.6.3. Output files cutadapt FastQC Picard CollectRnaSeqMetrics STAR and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID and fold changes/adjusted p values annotated by gene name Brain 3 per sample   RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   tissue:Brain 3 per sample|strain:TuAB|genotype:wildtype|treatment:n1|time:4 mpf GSM7102582 GSM7102582: Brain wildtype 4 mpf replicate 3 [15628X5]; Danio rerio; RNA Seq GSM7102582 r1 GSM7102582 1 RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP427757   loader:fastq load.py WT3_R1.fastq.gz WT3_R2.fastq.gz fastq fastq 16386006600.0 54258300.0 GSM7102582 r1 0:151 1:151 A:4682989185;C:3516688718;G:3618018588;T:4568150642;N:159467 151 151     4682989185 3516688718 3618018588 4568150642 159467 SRX19695584 SRS17064510 SRA1606419 Peterson, Pharmacology and Toxicology, University of Utah Peterson, Pharmacology and Toxicology, University of Utah 2 0.89215 0.89353 0.41753 0.41656 0.70672 0.70725 0.49029 0.48572 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion ribozero bulk bulk bulk   United States 2023-03-16 Adult Adult Brain Nervous System
74625 74625 SRR23883669 SRX19695583 SRS17064508 SRP427757 PRJNA945489 Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency GSE227551 Transcriptome Analysis Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality. To investigate the mechanisms driving saposin loss associated demyelination the brains of psap / zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene which codes for saposins A D. Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing and fish carrying the mutations of interest were propagated to homozygosity. RNA was isolated from the brains of four mpf psap / zebrafish and wildtype siblings.   pubmed:37183607   Brain psap knockout 4 mpf replicate 2 [15628X4] GSM7102581   source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf Brain psap knockout 4 mpf replicate 2 [15628X4] Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34 reads were trimmed of adapters using cutadapt 1.16 alignment was performed with STAR two pass mode and genes were assigned using featureCounts version 1.6.3. Output files cutadapt FastQC Picard CollectRnaSeqMetrics STAR and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID and fold changes/adjusted p values annotated by gene name Brain 3 per sample   RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf GSM7102581 GSM7102581: Brain psap knockout 4 mpf replicate 2 [15628X4]; Danio rerio; RNA Seq GSM7102581 r1 GSM7102581 1 RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP427757   loader:fastq load.py psap2_R1.fastq.gz psap2_R2.fastq.gz fastq fastq 15854933258.0 52499779.0 GSM7102581 r1 0:151 1:151 A:4570307174;C:3361185786;G:3477087934;T:4446197003;N:155361 151 151     4570307174 3361185786 3477087934 4446197003 155361 SRX19695583 SRS17064508 SRA1606419 Peterson, Pharmacology and Toxicology, University of Utah Peterson, Pharmacology and Toxicology, University of Utah 2 0.88921 0.88888 0.42958 0.42778 0.69096 0.69071 0.50225 0.50373 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion ribozero bulk bulk bulk   United States 2023-03-16 Adult Adult Brain Nervous System
74626 74626 SRR23883670 SRX19695582 SRS17064506 SRP427757 PRJNA945489 Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency GSE227551 Transcriptome Analysis Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality. To investigate the mechanisms driving saposin loss associated demyelination the brains of psap / zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene which codes for saposins A D. Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing and fish carrying the mutations of interest were propagated to homozygosity. RNA was isolated from the brains of four mpf psap / zebrafish and wildtype siblings.   pubmed:37183607   Brain wildtype 4 mpf replicate 2 [15628X3] GSM7102580   source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:wildtype|treatment:n1|time:4 mpf Brain wildtype 4 mpf replicate 2 [15628X3] Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34 reads were trimmed of adapters using cutadapt 1.16 alignment was performed with STAR two pass mode and genes were assigned using featureCounts version 1.6.3. Output files cutadapt FastQC Picard CollectRnaSeqMetrics STAR and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID and fold changes/adjusted p values annotated by gene name Brain 3 per sample   RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   tissue:Brain 3 per sample|strain:TuAB|genotype:wildtype|treatment:n1|time:4 mpf GSM7102580 GSM7102580: Brain wildtype 4 mpf replicate 2 [15628X3]; Danio rerio; RNA Seq GSM7102580 r1 GSM7102580 1 RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP427757   loader:fastq load.py WT2_R2.fastq.gz WT2_R1.fastq.gz fastq fastq 11602465218.0 38418759.0 GSM7102580 r1 0:151 1:151 A:3319702169;C:2467261858;G:2571507022;T:3243879933;N:114236 151 151     3319702169 2467261858 2571507022 3243879933 114236 SRX19695582 SRS17064506 SRA1606419 Peterson, Pharmacology and Toxicology, University of Utah Peterson, Pharmacology and Toxicology, University of Utah 2 0.77513 0.88687 0.38628 0.44686 0.72379 0.71003 0.48833 0.48813 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion ribozero bulk bulk bulk   United States 2023-03-16 Adult Adult Brain Nervous System
74627 74627 SRR23883671 SRX19695581 SRS17064509 SRP427757 PRJNA945489 Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency GSE227551 Transcriptome Analysis Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality. To investigate the mechanisms driving saposin loss associated demyelination the brains of psap / zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene which codes for saposins A D. Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing and fish carrying the mutations of interest were propagated to homozygosity. RNA was isolated from the brains of four mpf psap / zebrafish and wildtype siblings.   pubmed:37183607   Brain psap knockout 4 mpf replicate 1 [15628X2] GSM7102579   source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf Brain psap knockout 4 mpf replicate 1 [15628X2] Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34 reads were trimmed of adapters using cutadapt 1.16 alignment was performed with STAR two pass mode and genes were assigned using featureCounts version 1.6.3. Output files cutadapt FastQC Picard CollectRnaSeqMetrics STAR and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID and fold changes/adjusted p values annotated by gene name Brain 3 per sample   RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf GSM7102579 GSM7102579: Brain psap knockout 4 mpf replicate 1 [15628X2]; Danio rerio; RNA Seq GSM7102579 r1 GSM7102579 1 RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP427757   loader:fastq load.py psap1_R1.fastq.gz psap1_R2.fastq.gz fastq fastq 12758625408.0 42247104.0 GSM7102579 r1 0:151 1:151 A:3656266784;C:2715856446;G:2834432617;T:3551944161;N:125400 151 151     3656266784 2715856446 2834432617 3551944161 125400 SRX19695581 SRS17064509 SRA1606419 Peterson, Pharmacology and Toxicology, University of Utah Peterson, Pharmacology and Toxicology, University of Utah 2 0.88646 0.88808 0.43202 0.43202 0.68949 0.69094 0.50403 0.50436 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion ribozero bulk bulk bulk   United States 2023-03-16 Adult Adult Brain Nervous System
74628 74628 SRR23883672 SRX19695580 SRS17064507 SRP427757 PRJNA945489 Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency GSE227551 Transcriptome Analysis Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality. To investigate the mechanisms driving saposin loss associated demyelination the brains of psap / zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene which codes for saposins A D. Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing and fish carrying the mutations of interest were propagated to homozygosity. RNA was isolated from the brains of four mpf psap / zebrafish and wildtype siblings.   pubmed:37183607   Brain wildtype 4 mpf replicate 1 [15628X1] GSM7102578   source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:wildtype|treatment:n1|time:4 mpf Brain wildtype 4 mpf replicate 1 [15628X1] Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34 reads were trimmed of adapters using cutadapt 1.16 alignment was performed with STAR two pass mode and genes were assigned using featureCounts version 1.6.3. Output files cutadapt FastQC Picard CollectRnaSeqMetrics STAR and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID and fold changes/adjusted p values annotated by gene name Brain 3 per sample   RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   tissue:Brain 3 per sample|strain:TuAB|genotype:wildtype|treatment:n1|time:4 mpf GSM7102578 GSM7102578: Brain wildtype 4 mpf replicate 1 [15628X1]; Danio rerio; RNA Seq GSM7102578 r1 GSM7102578 1 RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP427757   loader:fastq load.py WT1_R1.fastq.gz WT1_R2.fastq.gz fastq fastq 14462198952.0 47888076.0 GSM7102578 r1 0:151 1:151 A:4136951572;C:3088385782;G:3192253341;T:4044465276;N:142981 151 151     4136951572 3088385782 3192253341 4044465276 142981 SRX19695580 SRS17064507 SRA1606419 Peterson, Pharmacology and Toxicology, University of Utah Peterson, Pharmacology and Toxicology, University of Utah 2 0.88554 0.88665 0.44368 0.44327 0.70897 0.70855 0.4979 0.49883 151 151 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion ribozero bulk bulk bulk   United States 2023-03-16 Adult Adult Brain Nervous System
75599 75599 SRR24709479 SRX20488149 SRS17798896 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     gata3 MO injected fish gata3 overexpression replicate 3 Gata3 rescue embryos replicate 3 HS3   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:Gata3 Morpholino OE|BioSampleModel:Model organism or animal                 Gata3 rescue embryos replicate 3 HS3 HS3 28 hpf zebrafish CNCC gata3 MO gata3 OE rep 3     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     hs-3_S44_L004_R1_001.fastq.gz hs-3_S44_L004_R2_001.fastq.gz fastq fastq 18826704764.0 62340082.0 hs 3 S44 L004 R1 001.fastq.gz 0:151 1:151 A:5114707285;C:4295423126;G:4475920802;T:4939819060;N:834491 151 151     5114707285 4295423126 4475920802 4939819060 834491 SRX20488149 SRS17798896 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.94567 0.95142 0.11234 0.11141 0.6983 0.69915 0.47093 0.47287 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System
75600 75600 SRR24709480 SRX20488148 SRS17798895 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     gata3 MO injected fish gata3 overexpression replicate 2 Gata3 rescue embryos replicate 2 HS2   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:Gata3 Mo OE|BioSampleModel:Model organism or animal                 Gata3 rescue embryos replicate 2 HS2 HS2 28 hpf zebrafish CNCC gata3 MO gata3 OE rep 2     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     hs-2_S43_L004_R1_001.fastq.gz hs-2_S43_L004_R2_001.fastq.gz fastq fastq 18888379506.0 62544303.0 hs 2 S43 L004 R1 001.fastq.gz 0:151 1:151 A:5096840826;C:4346330631;G:4477598678;T:4966787816;N:821555 151 151     5096840826 4346330631 4477598678 4966787816 821555 SRX20488148 SRS17798895 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.94359 0.95104 0.10627 0.10498 0.69775 0.69645 0.46042 0.46973 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System
75601 75601 SRR24709481 SRX20488147 SRS17798894 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     gata3 MO injected fish gata3 overexpression replicate 1 Gata3 rescue embryos replicate 1 HS1   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:Gata3 MO OE|BioSampleModel:Model organism or animal                 Gata3 rescue embryos replicate 1 HS1 HS1 28 hpf zebrafish CNCC gata3 MO gata3 OE rep 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     hs-1_S42_L004_R1_001.fastq.gz hs-1_S42_L004_R2_001.fastq.gz fastq fastq 25741814090.0 85237795.0 hs 1 S42 L004 R1 001.fastq.gz 0:151 1:151 A:6965410653;C:5925601348;G:6079527023;T:6770131607;N:1143459 151 151     6965410653 5925601348 6079527023 6770131607 1143459 SRX20488147 SRS17798894 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.95099 0.9551 0.09834 0.09834 0.69739 0.69718 0.47103 0.47222 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System
75602 75602 SRR24709482 SRX20488146 SRS17798893 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     gata3 MO injected fish replicate 3 Gata3 KD embryos replicate 3 Mo3   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:Gata3 Morpholino|BioSampleModel:Model organism or animal                 Gata3 KD embryos replicate 3 Mo3 Mo3 28 hpf zebrafish CNCC gata3 MO rep 3     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     g3-3_S38_L004_R1_001.fastq.gz g3-3_S38_L004_R2_001.fastq.gz fastq fastq 21393818316.0 70840458.0 g3 3 S38 L004 R1 001.fastq.gz 0:151 1:151 A:5727292905;C:4958373450;G:5148761848;T:5558495738;N:894375 151 151     5727292905 4958373450 5148761848 5558495738 894375 SRX20488146 SRS17798893 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.95248 0.9562 0.09502 0.09436 0.69919 0.69996 0.4892 0.48787 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System
75603 75603 SRR24709483 SRX20488145 SRS17798892 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     gata3 MO injected fish replicate 2 Gata3 KD embryos replicate 2 Mo2   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:Gata3 Mo|BioSampleModel:Model organism or animal                 Gata3 KD embryos replicate 2 Mo2 Mo2 28 hpf zebrafish CNCC gata3 MO rep 2     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     g3-2_S37_L004_R1_001.fastq.gz g3-2_S37_L004_R2_001.fastq.gz fastq fastq 21351583314.0 70700607.0 g3 2 S37 L004 R1 001.fastq.gz 0:151 1:151 A:5735386416;C:4940166804;G:5132607187;T:5542503685;N:919222 151 151     5735386416 4940166804 5132607187 5542503685 919222 SRX20488145 SRS17798892 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.95082 0.95484 0.09993 0.0994 0.69936 0.69927 0.48687 0.49169 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System
75604 75604 SRR24709484 SRX20488144 SRS17798891 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     gata3 MO injected fish replicate 1 Gata3 KD embryos replicate 1 Mo1   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:Gata3 MO|BioSampleModel:Model organism or animal                 Gata3 KD embryos replicate 1 Mo1 Mo1 28 hpf zebrafish CNCC gata3 MO rep 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     g3-1_S36_L004_R1_001.fastq.gz g3-1_S36_L004_R2_001.fastq.gz fastq fastq 28547080614.0 94526757.0 g3 1 S36 L004 R1 001.fastq.gz 0:151 1:151 A:7702457862;C:6587896625;G:6810525192;T:7444946485;N:1254450 151 151     7702457862 6587896625 6810525192 7444946485 1254450 SRX20488144 SRS17798891 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.95229 0.95421 0.09736 0.0951 0.69909 0.69954 0.4751 0.47584 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System
75605 75605 SRR24709485 SRX20488143 SRS17798890 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     Uninjected fish replicate 3 Control embryos replicate 3 Control3   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:No morpholino|BioSampleModel:Model organism or animal                 Control embryos replicate 3 Control3 Control3 28 hpf zebrafish CNCC no MO rep 3     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     con-3_S41_L004_R1_001.fastq.gz con-3_S41_L004_R2_001.fastq.gz fastq fastq 15957361994.0 52838947.0 con 3 S41 L004 R1 001.fastq.gz 0:151 1:151 A:4353252985;C:3627865851;G:3741979504;T:4233577428;N:686226 151 151     4353252985 3627865851 3741979504 4233577428 686226 SRX20488143 SRS17798890 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.94977 0.95285 0.10662 0.1056 0.69613 0.69613 0.47705 0.47245 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System
75606 75606 SRR24709486 SRX20488142 SRS17798889 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     Uninjected fish replicate 2 Control embryos replicate 2 Control2   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:No Mo|BioSampleModel:Model organism or animal                 Control embryos replicate 2 Control2 Control2 28 hpf zebrafish CNCC no MO rep 2     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     con-2_S40_L004_R1_001.fastq.gz con-2_S40_L004_R2_001.fastq.gz fastq fastq 20993966994.0 69516447.0 con 2 S40 L004 R1 001.fastq.gz 0:151 1:151 A:5568327305;C:4941751779;G:5092661056;T:5390404217;N:822637 151 151     5568327305 4941751779 5092661056 5390404217 822637 SRX20488142 SRS17798889 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.9531 0.86099 0.11979 0.10492 0.70205 0.71196 0.4954 0.50148 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System
75607 75607 SRR24709487 SRX20488141 SRS17798888 SRP439167 PRJNA975174 Bulk RNA seq investigating differential gene regulation across gata3 knockdown and rescue PRJNA975174 Other Loss of the transcription factor Gata3 associates with the highly variable human birth defects HDR syndrome and microsomia and can lead to disruption of the neural crest derived facial skeleton. RNA was isolated from cranial neural crest cells of zebrafish embryos at 28 hpf in control gata3 knockdown and gata3 overexpression embryos. Goal of the study was to illustrate multiple potential pathways for Gata3 function and demonstrate a systematic unbiased process to identify modifiers of genotype phenotype correlations.     Uninjected fish replicate 1 Control embryos replicate 1 Control1   strain:Not collected|isolate:Not collected|breed:Not collected|cultivar:Not collected|ecotype:Not collected|age:Not determined|dev stage:28 hpf|sex:Not determined|tissue:Cranial neural crest cells|treatment:No MO|BioSampleModel:Model organism or animal                 Control embryos replicate 1 Control1 Control1 28 hpf zebrafish CNCC no MO rep 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439167     con-1_S39_L004_R1_001.fastq.gz con-1_S39_L004_R2_001.fastq.gz fastq fastq 26059573658.0 86289979.0 con 1 S39 L004 R1 001.fastq.gz 0:151 1:151 A:6956736272;C:6114717013;G:6342229191;T:6644732877;N:1158305 151 151     6956736272 6114717013 6342229191 6644732877 1158305 SRX20488141 SRS17798888 SRA1643035 University of Texas at Austin|Department of Molecular Biosciences University of Texas at Austin 2 0.95466 0.95558 0.10068 0.09865 0.7025 0.7035 0.49494 0.49368 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-05-23 Pharyngula Embryo Brain Nervous System

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