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148 rows where technology = "bulk" and tissue_curation = "Brain"

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devstage_curation 7

devstage_curation_coarse 6

experiment.library_selection 4

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Brain · 148 ✖

technology 1

  • bulk · 148 ✖

experiment.platform 1

experiment.library_source 1

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
28692 28692 SRR26535343 SRX22238470 SRS19292731 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2 GSM7866394   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2 Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866394 GSM7866394: EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2; Danio rerio; RNA Seq GSM7866394 r1 GSM7866394 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py CTRL_3.fastq.gz fastq 7081948098.0 70118298.0 GSM7866394 r1 0:101 A:1894557984;C:1627945034;G:1550203852;T:2009224463;N:16765 101       1894557984 1627945034 1550203852 2009224463 16765 SRX22238470 SRS19292731 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.94543   0.14646   0.68883   0.49451   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
28693 28693 SRR26535344 SRX22238469 SRS19292730 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1 GSM7866393   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1 Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866393 GSM7866393: EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1; Danio rerio; RNA Seq GSM7866393 r1 GSM7866393 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py CTRL_2.fastq.gz fastq 7840572329.0 77629429.0 GSM7866393 r1 0:101 A:2099360211;C:1783653297;G:1717681461;T:2239858766;N:18594 101       2099360211 1783653297 1717681461 2239858766 18594 SRX22238469 SRS19292730 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.93984   0.1663   0.69033   0.484   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
28694 28694 SRR26535345 SRX22238468 SRS19292729 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   KRAS PI3KCAH1047R GFP tumor negative control brain GSM7866392   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing KRAS PI3KCAH1047R GFP tumor negative control brain Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866392 GSM7866392: KRAS PI3KCAH1047R GFP tumor negative control brain; Danio rerio; RNA Seq GSM7866392 r1 GSM7866392 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py CTRL_1.fastq.gz fastq 10164914720.0 100642720.0 GSM7866392 r1 0:101 A:2650336113;C:2354113843;G:2276252979;T:2884188285;N:23500 101       2650336113 2354113843 2276252979 2884188285 23500 SRX22238468 SRS19292729 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.94271   0.10831   0.68527   0.50207   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
28695 28695 SRR26535346 SRX22238467 SRS19292728 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3 GSM7866391   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3 Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866391 GSM7866391: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3; Danio rerio; RNA Seq GSM7866391 r1 GSM7866391 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py EPS_3.fastq.gz fastq 9796714170.0 96997170.0 GSM7866391 r1 0:101 A:2627522717;C:2223655583;G:2134761894;T:2810751194;N:22782 101       2627522717 2223655583 2134761894 2810751194 22782 SRX22238467 SRS19292728 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.92543   0.1876   0.67308   0.4886   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
28696 28696 SRR26535347 SRX22238466 SRS19292727 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2 GSM7866390   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2 Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866390 GSM7866390: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2; Danio rerio; RNA Seq GSM7866390 r1 GSM7866390 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py EPS_2.fastq.gz fastq 7839595861.0 77619761.0 GSM7866390 r1 0:101 A:2093456023;C:1792947580;G:1718784421;T:2234389453;N:18384 101       2093456023 1792947580 1718784421 2234389453 18384 SRX22238466 SRS19292727 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.93807   0.14978   0.68854   0.47786   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
28697 28697 SRR26535348 SRX22238465 SRS19292726 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1 GSM7866389   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1 Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866389 GSM7866389: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1; Danio rerio; RNA Seq GSM7866389 r1 GSM7866389 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py EPS_1.fastq.gz fastq 8403475528.0 83202728.0 GSM7866389 r1 0:101 A:2217465507;C:1940028683;G:1857031218;T:2388930530;N:19590 101       2217465507 1940028683 1857031218 2388930530 19590 SRX22238465 SRS19292726 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.94596   0.12916   0.68619   0.4957   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
28698 28698 SRR26535349 SRX22238464 SRS19292725 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   KRAS PI3KCAH1047R GFP tumor positive whole brain 3 GSM7866388   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing KRAS PI3KCAH1047R GFP tumor positive whole brain 3 Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866388 GSM7866388: KRAS PI3KCAH1047R GFP tumor positive whole brain 3; Danio rerio; RNA Seq GSM7866388 r1 GSM7866388 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py KPG_3.fastq.gz fastq 7609183450.0 75338450.0 GSM7866388 r1 0:101 A:2040241047;C:1721563382;G:1666400346;T:2180961056;N:17619 101       2040241047 1721563382 1666400346 2180961056 17619 SRX22238464 SRS19292725 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.93555   0.16895   0.68199   0.50032   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
28699 28699 SRR26535350 SRX22238463 SRS19292724 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   KRAS PI3KCAH1047R GFP tumor positive whole brain 2 GSM7866387   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing KRAS PI3KCAH1047R GFP tumor positive whole brain 2 Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866387 GSM7866387: KRAS PI3KCAH1047R GFP tumor positive whole brain 2; Danio rerio; RNA Seq GSM7866387 r1 GSM7866387 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py KPG_2.fastq.gz fastq 8446573339.0 83629439.0 GSM7866387 r1 0:101 A:2223763293;C:1944013929;G:1869828652;T:2408947564;N:19901 101       2223763293 1944013929 1869828652 2408947564 19901 SRX22238463 SRS19292724 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.94943   0.11539   0.68428   0.51019   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
28700 28700 SRR26535351 SRX22238462 SRS19292723 SRP468564 PRJNA1032461 A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo GSE246295 Transcriptome Analysis To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…   pubmed:39052000   KRAS PI3KCAH1047R GFP tumor positive whole brain 1 GSM7866386   source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing KRAS PI3KCAH1047R GFP tumor positive whole brain 1 Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions. Whole Brain Fertilized embryos injected with either EPS or KPG construct mix Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations Zebrafish were housed and reared following approved animal use protocol strain:CG1 p53null|tissue:Whole Brain GSM7866386 GSM7866386: KRAS PI3KCAH1047R GFP tumor positive whole brain 1; Danio rerio; RNA Seq GSM7866386 r1 GSM7866386 1 Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP468564   loader:fastq load.py KPG_1.fastq.gz fastq 4326209053.0 42833753.0 GSM7866386 r1 0:101 A:1143856405;C:993993009;G:951829931;T:1236519669;N:10039 101       1143856405 993993009 951829931 1236519669 10039 SRX22238462 SRS19292723 SRA1740017 Hayes Lab, DSCB, Sickkids Research Hayes Lab, DSCB, Sickkids Research 1 0.94443   0.13057   0.68503   0.50149   101   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Canada 2023-10-26 Undetermined Embryo Brain Nervous System
43758 43758 SRR6072798 SRX3214272 SRS2539011 SRP118819 PRJNA412050 Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio GSE104221 Other The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.   pubmed:29686887   PCB126 BRAIN4 RNA Seq GSM2792798   tissue:brain|treatment:PCB126|life history stage:Adult PCB126 BRAIN4 RNA Seq Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls. brain Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues. Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.   treatment:PCB126|life history stage:Adult GSM2792798 GSM2792798: PCB126 BRAIN4 RNA Seq; Danio rerio; RNA Seq GSM2792798   1 Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit. GEO Accession:GSM2792798 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP118819     PB4_S16_L002_R1_001.fastq.gz fastq 1375628508.0 26973108.0 GSM2792798 r1 0:51 1:0 A:389260936;C:298336750;G:285290157;T:402727589;N:13076 51 0     389260936 298336750 285290157 402727589 13076 SRX3214272 SRS2539011 SRA612796 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.90102   0.20673   0.69152   0.51941   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2017-09-25 Adult Adult Brain Nervous System
43759 43759 SRR6072797 SRX3214271 SRS2539012 SRP118819 PRJNA412050 Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio GSE104221 Other The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.   pubmed:29686887   PCB126 BRAIN3 RNA Seq GSM2792797   tissue:brain|treatment:PCB126|life history stage:Adult PCB126 BRAIN3 RNA Seq Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls. brain Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues. Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.   treatment:PCB126|life history stage:Adult GSM2792797 GSM2792797: PCB126 BRAIN3 RNA Seq; Danio rerio; RNA Seq GSM2792797   1 Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit. GEO Accession:GSM2792797 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP118819     PB3_S15_L002_R1_001.fastq.gz fastq 1534214028.0 30082628.0 GSM2792797 r1 0:51 1:0 A:434098364;C:333114785;G:318943720;T:448043305;N:13854 51 0     434098364 333114785 318943720 448043305 13854 SRX3214271 SRS2539012 SRA612796 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.88591   0.19161   0.67967   0.53267   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2017-09-25 Adult Adult Brain Nervous System
43760 43760 SRR6072796 SRX3214270 SRS2539009 SRP118819 PRJNA412050 Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio GSE104221 Other The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.   pubmed:29686887   PCB126 BRAIN2 RNA Seq GSM2792796   tissue:brain|treatment:PCB126|life history stage:Adult PCB126 BRAIN2 RNA Seq Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls. brain Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues. Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.   treatment:PCB126|life history stage:Adult GSM2792796 GSM2792796: PCB126 BRAIN2 RNA Seq; Danio rerio; RNA Seq GSM2792796   1 Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit. GEO Accession:GSM2792796 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP118819     PB2_S14_L002_R1_001.fastq.gz fastq 1492641276.0 29267476.0 GSM2792796 r1 0:51 1:0 A:419506485;C:327077186;G:314622527;T:431420803;N:14275 51 0     419506485 327077186 314622527 431420803 14275 SRX3214270 SRS2539009 SRA612796 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.89327   0.18282   0.68777   0.53375   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2017-09-25 Adult Adult Brain Nervous System
43761 43761 SRR6072795 SRX3214269 SRS2539010 SRP118819 PRJNA412050 Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio GSE104221 Other The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.   pubmed:29686887   PCB126 BRAIN1 RNA Seq GSM2792795   tissue:brain|treatment:PCB126|life history stage:Adult PCB126 BRAIN1 RNA Seq Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls. brain Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues. Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.   treatment:PCB126|life history stage:Adult GSM2792795 GSM2792795: PCB126 BRAIN1 RNA Seq; Danio rerio; RNA Seq GSM2792795   1 Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit. GEO Accession:GSM2792795 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP118819     PB1_S13_L002_R1_001.fastq.gz fastq 1540239576.0 30200776.0 GSM2792795 r1 0:51 1:0 A:425532690;C:346041208;G:332010797;T:436640179;N:14702 51 0     425532690 346041208 332010797 436640179 14702 SRX3214269 SRS2539010 SRA612796 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.8846   0.14495   0.67142   0.51907   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2017-09-25 Adult Adult Brain Nervous System
43762 43762 SRR6072794 SRX3214268 SRS2539008 SRP118819 PRJNA412050 Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio GSE104221 Other The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.   pubmed:29686887   CONTROL BRAIN4 RNA Seq GSM2792794   tissue:brain|treatment:DMSO|life history stage:Adult CONTROL BRAIN4 RNA Seq Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls. brain Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues. Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.   treatment:DMSO|life history stage:Adult GSM2792794 GSM2792794: CONTROL BRAIN4 RNA Seq; Danio rerio; RNA Seq GSM2792794   1 Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit. GEO Accession:GSM2792794 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP118819     CB4_S12_L002_R1_001.fastq.gz fastq 1463255535.0 28691285.0 GSM2792794 r1 0:51 1:0 A:408992269;C:323726908;G:309480781;T:421041726;N:13851 51 0     408992269 323726908 309480781 421041726 13851 SRX3214268 SRS2539008 SRA612796 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.89686   0.19559   0.69871   0.50956   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2017-09-25 Adult Adult Brain Nervous System
43763 43763 SRR6072793 SRX3214267 SRS2539124 SRP118819 PRJNA412050 Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio GSE104221 Other The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.   pubmed:29686887   CONTROL BRAIN3 RNA Seq GSM2792793   tissue:brain|treatment:DMSO|life history stage:Adult CONTROL BRAIN3 RNA Seq Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls. brain Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues. Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.   treatment:DMSO|life history stage:Adult GSM2792793 GSM2792793: CONTROL BRAIN3 RNA Seq; Danio rerio; RNA Seq GSM2792793   1 Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit. GEO Accession:GSM2792793 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP118819     CB3_S11_L002_R1_001.fastq.gz fastq 1624268910.0 31848410.0 GSM2792793 r1 0:51 1:0 A:452040960;C:360441413;G:344970351;T:466800984;N:15202 51 0     452040960 360441413 344970351 466800984 15202 SRX3214267 SRS2539124 SRA612796 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.89974   0.19642   0.6896   0.49428   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2017-09-25 Adult Adult Brain Nervous System
43764 43764 SRR6072792 SRX3214266 SRS2539123 SRP118819 PRJNA412050 Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio GSE104221 Other The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.   pubmed:29686887   CONTROL BRAIN2 RNA Seq GSM2792792   tissue:brain|treatment:DMSO|life history stage:Adult CONTROL BRAIN2 RNA Seq Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls. brain Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues. Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.   treatment:DMSO|life history stage:Adult GSM2792792 GSM2792792: CONTROL BRAIN2 RNA Seq; Danio rerio; RNA Seq GSM2792792   1 Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit. GEO Accession:GSM2792792 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP118819     CB2_S10_L002_R1_001.fastq.gz fastq 1740210678.0 34121778.0 GSM2792792 r1 0:51 1:0 A:480819797;C:388942062;G:374434527;T:495998198;N:16094 51 0     480819797 388942062 374434527 495998198 16094 SRX3214266 SRS2539123 SRA612796 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.91021   0.19053   0.68603   0.4987   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2017-09-25 Adult Adult Brain Nervous System
43765 43765 SRR6072791 SRX3214265 SRS2539120 SRP118819 PRJNA412050 Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio GSE104221 Other The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.   pubmed:29686887   CONTROL BRAIN1 RNA Seq GSM2792791   tissue:brain|treatment:DMSO|life history stage:Adult CONTROL BRAIN1 RNA Seq Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls. brain Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues. Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.   treatment:DMSO|life history stage:Adult GSM2792791 GSM2792791: CONTROL BRAIN1 RNA Seq; Danio rerio; RNA Seq GSM2792791   1 Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit. GEO Accession:GSM2792791 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP118819     CB1_S9_L002_R1_001.fastq.gz fastq 1715146677.0 33630327.0 GSM2792791 r1 0:51 1:0 A:476861764;C:381757171;G:366051176;T:490460394;N:16172 51 0     476861764 381757171 366051176 490460394 16172 SRX3214265 SRS2539120 SRA612796 GEO Aluru Lab, Biology, Woods Hole Oceanographic Institution 1 0.90508   0.18823   0.69607   0.51563   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2017-09-25 Adult Adult Brain Nervous System
53249 53249 SRR9825129 SRX6581798 SRS5147496 SRP216250 PRJNA556200 Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq GSE134705 Other Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. parent bioproject:PRJNA556197 pubmed:31835035   AB7155 GSM3963895   source name:Total brain|strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|age:4 5mo AB7155 bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while "NNNNNN" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample Total brain   Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014}   strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|catalog#:I32450|age:4 5mo GSM3963895 GSM3963895: AB7155; Danio rerio; RNA Seq GSM3963895   1 Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014} GEO Accession:GSM3963895 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP216250   loader:fastq load.py|options: appendBCtoName AB7155_SB343_S29_R1_001.fastq.gz fastq 1139724267.0 16517743.0 GSM3963895 r1 0:69 A:331549647;C:254056286;G:280458785;T:273550294;N:109255 69       331549647 254056286 280458785 273550294 109255 SRX6581798 SRS5147496 SRA926018 GEO Immunology, Weizmann Institute of Science 1 0.90535   0.17532   0.87803   0.67683   69   B   usable mapping rate illumina nextseq unknown poly_a unknown sc_generic bulk bulk   Israel 2019-07-23 Undetermined Undetermined Brain Nervous System
53250 53250 SRR9825128 SRX6581797 SRS5147495 SRP216250 PRJNA556200 Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq GSE134705 Other Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. parent bioproject:PRJNA556197 pubmed:31835035   AB7154 GSM3963894   source name:Total brain|strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|age:4 5mo AB7154 bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while "NNNNNN" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample Total brain   Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014}   strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|catalog#:I32450|age:4 5mo GSM3963894 GSM3963894: AB7154; Danio rerio; RNA Seq GSM3963894   1 Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014} GEO Accession:GSM3963894 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP216250   loader:fastq load.py|options: appendBCtoName AB7154_SB343_S36_R1_001.fastq.gz fastq 1161384609.0 16831661.0 GSM3963894 r1 0:69 A:337010566;C:261723350;G:290674768;T:271864761;N:111164 69       337010566 261723350 290674768 271864761 111164 SRX6581797 SRS5147495 SRA926018 GEO Immunology, Weizmann Institute of Science 1 0.89031   0.18199   0.88154   0.67975   69   B   usable mapping rate illumina nextseq unknown poly_a unknown sc_generic bulk bulk   Israel 2019-07-23 Undetermined Undetermined Brain Nervous System
53251 53251 SRR9825127 SRX6581796 SRS5147494 SRP216250 PRJNA556200 Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq GSE134705 Other Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. parent bioproject:PRJNA556197 pubmed:31835035   AB7153 GSM3963893   source name:Total brain|strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|age:4 5mo AB7153 bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while "NNNNNN" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample Total brain   Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014}   strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|catalog#:I32450|age:4 5mo GSM3963893 GSM3963893: AB7153; Danio rerio; RNA Seq GSM3963893   1 Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014} GEO Accession:GSM3963893 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP216250   loader:fastq load.py|options: appendBCtoName AB7153_SB343_S44_R1_001.fastq.gz fastq 1088811030.0 15779870.0 GSM3963893 r1 0:69 A:320167297;C:243538818;G:266263775;T:258739754;N:101386 69       320167297 243538818 266263775 258739754 101386 SRX6581796 SRS5147494 SRA926018 GEO Immunology, Weizmann Institute of Science 1 0.89179   0.12861   0.87259   0.63828   69   B   usable mapping rate illumina nextseq unknown poly_a unknown sc_generic bulk bulk   Israel 2019-07-23 Undetermined Undetermined Brain Nervous System
53252 53252 SRR9825125 SRX6581795 SRS5147493 SRP216250 PRJNA556200 Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq GSE134705 Other Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. parent bioproject:PRJNA556197 pubmed:31835035   AB5657 GSM3963892   source name:Total brain|strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|age:4 5mo AB5657 bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while "NNNNNN" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample Total brain   Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014}   strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|catalog#:NA|age:4 5mo GSM3963892 GSM3963892: AB5657; Danio rerio; RNA Seq GSM3963892   1 Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014} GEO Accession:GSM3963892 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP216250   loader:fastq load.py|options: appendBCtoName AB5657_SB283_S14_R1_001.fastq.gz fastq 331332549.0 4801921.0 GSM3963892 r1 0:69 A:89857088;C:69771659;G:81302142;T:90395650;N:6010 69       89857088 69771659 81302142 90395650 6010 SRX6581795 SRS5147493 SRA926018 GEO Immunology, Weizmann Institute of Science 1 0.88981   0.33973   0.93507   0.6341   69   B   usable mapping rate illumina nextseq unknown poly_a unknown sc_generic bulk bulk   Israel 2019-07-23 Undetermined Undetermined Brain Nervous System
53253 53253 SRR9825126 SRX6581795 SRS5147493 SRP216250 PRJNA556200 Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq GSE134705 Other Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. parent bioproject:PRJNA556197 pubmed:31835035   AB5657 GSM3963892   source name:Total brain|strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|age:4 5mo AB5657 bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while "NNNNNN" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample Total brain   Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014}   strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|catalog#:NA|age:4 5mo GSM3963892 GSM3963892: AB5657; Danio rerio; RNA Seq GSM3963892   1 Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014} GEO Accession:GSM3963892 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP216250   loader:fastq load.py|options: appendBCtoName AB5657_SB284_S3_R1_001.fastq.gz fastq 796908117.0 11549393.0 GSM3963892 r2 0:69 A:223319161;C:173475726;G:194239433;T:205842249;N:31548 69       223319161 173475726 194239433 205842249 31548 SRX6581795 SRS5147493 SRA926018 GEO Immunology, Weizmann Institute of Science 1 0.8909   0.30223   0.91802   0.65318   69   B   usable mapping rate illumina nextseq unknown poly_a unknown sc_generic bulk bulk   Israel 2019-07-23 Undetermined Undetermined Brain Nervous System
53254 53254 SRR9825124 SRX6581794 SRS5147492 SRP216250 PRJNA556200 Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq GSE134705 Other Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. parent bioproject:PRJNA556197 pubmed:31835035   AB3014 GSM3963891   source name:Total brain|strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|age:4 5mo AB3014 bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while "NNNNNN" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample Total brain   Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014}   strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|catalog#:NA|age:4 5mo GSM3963891 GSM3963891: AB3014; Danio rerio; RNA Seq GSM3963891   1 Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014} GEO Accession:GSM3963891 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP216250   loader:fastq load.py|options: appendBCtoName AB3014.fastq.gz fastq 1854197730.0 28093905.0 GSM3963891 r1 0:66 A:546306466;C:392206824;G:436944803;T:478712291;N:27346 66       546306466 392206824 436944803 478712291 27346 SRX6581794 SRS5147492 SRA926018 GEO Immunology, Weizmann Institute of Science 1 0.90278   0.4347   0.88925   0.64871   66   B   usable mapping rate illumina nextseq unknown poly_a unknown sc_generic bulk bulk   Israel 2019-07-23 Undetermined Undetermined 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
61837 61837 SRR12999696 SRX9450941 SRS7663855 SRP291443 PRJNA675087 MicroRNAs involved in regeneration of adult zebrafish brain. GSE160992 Transcriptome Analysis For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere   pubmed:34054419;pubmed:35204047   injured telencephalic hemisphere 3 GSM4887529   source name:telencephalic hemisphere|tissue:telencephalon|treatment:injury injured telencephalic hemisphere 3 Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene telencephalic hemisphere   Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.   tissue:telencephalon|treatment:injury GSM4887529 GSM4887529: injured telencephalic hemisphere 3; Danio rerio; RNA Seq GSM4887529   1 Trizol Invitrogen TrueSeq RNA Illumina GEO Accession:GSM4887529 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP291443     STAB3.fastq.gz fastq 1424796409.0 65132630.0 GSM4887529 r1 0:21.88 1:0 A:333355914;C:282050013;G:361225960;T:448164522;N:0 21 0     333355914 282050013 361225960 448164522 0 SRX9450941 SRS7663855 SRA1155190 GEO UMR1064, Centre de recherche en transplantation et immunologie 1 0.92334   0.08864   0.97611   0.54523   22   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Canada 2020-11-06 Undetermined Adult Brain Nervous System
61838 61838 SRR12999695 SRX9450940 SRS7663854 SRP291443 PRJNA675087 MicroRNAs involved in regeneration of adult zebrafish brain. GSE160992 Transcriptome Analysis For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere   pubmed:34054419;pubmed:35204047   injured telencephalic hemisphere 2 GSM4887528   source name:telencephalic hemisphere|tissue:telencephalon|treatment:injury injured telencephalic hemisphere 2 Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene telencephalic hemisphere   Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.   tissue:telencephalon|treatment:injury GSM4887528 GSM4887528: injured telencephalic hemisphere 2; Danio rerio; RNA Seq GSM4887528   1 Trizol Invitrogen TrueSeq RNA Illumina GEO Accession:GSM4887528 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP291443     STAB2.fastq.gz fastq 1492088541.0 67892332.0 GSM4887528 r1 0:21.98 1:0 A:349593244;C:293016325;G:377668555;T:471810417;N:0 21 0     349593244 293016325 377668555 471810417 0 SRX9450940 SRS7663854 SRA1155190 GEO UMR1064, Centre de recherche en transplantation et immunologie 1 0.93253   0.08588   0.97666   0.54494   22   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Canada 2020-11-06 Undetermined Adult Brain Nervous System
61839 61839 SRR12999694 SRX9450939 SRS7663853 SRP291443 PRJNA675087 MicroRNAs involved in regeneration of adult zebrafish brain. GSE160992 Transcriptome Analysis For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere   pubmed:34054419;pubmed:35204047   injured telencephalic hemisphere 1 GSM4887527   source name:telencephalic hemisphere|tissue:telencephalon|treatment:injury injured telencephalic hemisphere 1 Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene telencephalic hemisphere   Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.   tissue:telencephalon|treatment:injury GSM4887527 GSM4887527: injured telencephalic hemisphere 1; Danio rerio; RNA Seq GSM4887527   1 Trizol Invitrogen TrueSeq RNA Illumina GEO Accession:GSM4887527 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP291443     STAB1.fastq.gz fastq 1915689209.0 87803695.0 GSM4887527 r1 0:21.82 1:0 A:446653242;C:378509659;G:482923940;T:607602368;N:0 21 0     446653242 378509659 482923940 607602368 0 SRX9450939 SRS7663853 SRA1155190 GEO UMR1064, Centre de recherche en transplantation et immunologie 1 0.91949   0.08917   0.97954   0.53009   21   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Canada 2020-11-06 Undetermined Adult Brain Nervous System
61840 61840 SRR12999693 SRX9450938 SRS7663852 SRP291443 PRJNA675087 MicroRNAs involved in regeneration of adult zebrafish brain. GSE160992 Transcriptome Analysis For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere   pubmed:34054419;pubmed:35204047   healthy telencephalic hemisphere 3 GSM4887526   source name:telencephalic hemisphere|tissue:telencephalon|treatment:no treatment healthy telencephalic hemisphere 3 Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene telencephalic hemisphere   Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.   tissue:telencephalon|treatment:no treatment GSM4887526 GSM4887526: healthy telencephalic hemisphere 3; Danio rerio; RNA Seq GSM4887526   1 Trizol Invitrogen TrueSeq RNA Illumina GEO Accession:GSM4887526 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP291443     CTRL3.fastq.gz fastq 323568644.0 14847336.0 GSM4887526 r1 0:21.79 1:0 A:75720892;C:64438959;G:80940855;T:102467938;N:0 21 0     75720892 64438959 80940855 102467938 0 SRX9450938 SRS7663852 SRA1155190 GEO UMR1064, Centre de recherche en transplantation et immunologie 1 0.91791   0.08755   0.98054   0.5616   22   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Canada 2020-11-06 Undetermined Adult Brain Nervous System
61841 61841 SRR12999692 SRX9450937 SRS7663851 SRP291443 PRJNA675087 MicroRNAs involved in regeneration of adult zebrafish brain. GSE160992 Transcriptome Analysis For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere   pubmed:34054419;pubmed:35204047   healthy telencephalic hemisphere 2 GSM4887525   source name:telencephalic hemisphere|tissue:telencephalon|treatment:no treatment healthy telencephalic hemisphere 2 Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene telencephalic hemisphere   Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.   tissue:telencephalon|treatment:no treatment GSM4887525 GSM4887525: healthy telencephalic hemisphere 2; Danio rerio; RNA Seq GSM4887525   1 Trizol Invitrogen TrueSeq RNA Illumina GEO Accession:GSM4887525 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP291443     CTRL2.fastq.gz fastq 533253402.0 24364720.0 GSM4887525 r1 0:21.89 1:0 A:125553872;C:106408524;G:133237076;T:168053930;N:0 21 0     125553872 106408524 133237076 168053930 0 SRX9450937 SRS7663851 SRA1155190 GEO UMR1064, Centre de recherche en transplantation et immunologie 1 0.92261   0.08906   0.97881   0.55986   21   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Canada 2020-11-06 Undetermined Adult Brain Nervous System
61842 61842 SRR12999691 SRX9450936 SRS7663850 SRP291443 PRJNA675087 MicroRNAs involved in regeneration of adult zebrafish brain. GSE160992 Transcriptome Analysis For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere   pubmed:34054419;pubmed:35204047   healthy telencephalic hemisphere 1 GSM4887524   source name:telencephalic hemisphere|tissue:telencephalon|treatment:no treatment healthy telencephalic hemisphere 1 Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene telencephalic hemisphere   Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.   tissue:telencephalon|treatment:no treatment GSM4887524 GSM4887524: healthy telencephalic hemisphere 1; Danio rerio; RNA Seq GSM4887524   1 Trizol Invitrogen TrueSeq RNA Illumina GEO Accession:GSM4887524 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP291443     CTRL1.fastq.gz fastq 347713277.0 15928765.0 GSM4887524 r1 0:21.83 1:0 A:81497309;C:69157722;G:86472353;T:110585893;N:0 21 0     81497309 69157722 86472353 110585893 0 SRX9450936 SRS7663850 SRA1155190 GEO UMR1064, Centre de recherche en transplantation et immunologie 1 0.91979   0.0902   0.96512   0.56094   22   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Canada 2020-11-06 Undetermined Adult 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

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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");;