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240 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "bulk" and tissue_curation_coarse = "Nervous System"

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devstage_curation 8

devstage_curation_coarse 6

experiment.library_selection 5

tissue_curation 3

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Nervous System · 240 ✖

technology 1

  • bulk · 240 ✖

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 240 ✖
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
34192 34192 SRR31443228 SRX26812023 SRS23296672 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 3   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 3 srrm4[y712] mutant replicate 3 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut3.pass2Aligned.sortedByCoord.out.bam bam 23466336192.0 117587529.0 25938 mut3.pass2Aligned.sortedByCoord.out.bam 0:100.13 1:100.08 A:6298034402;C:5433884683;G:5344985734;T:6388443446;N:987927 100 100     6298034402 5433884683 5344985734 6388443446 987927 SRX26812023 SRS23296672 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.95864 0.95894 0.10681 0.1052 0.65385 0.65403 0.46511 0.46252 99 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34193 34193 SRR31443229 SRX26812022 SRS23296671 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 3   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 3 srrm4[y712] wild type replicate 3 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt3.pass2Aligned.sortedByCoord.out.bam bam 23979171134.0 120156039.0 25938 wt3.pass2Aligned.sortedByCoord.out.bam 0:100.12 1:100.07 A:6398807397;C:5589997524;G:5503127729;T:6486232627;N:1005857 100 100     6398807397 5589997524 5503127729 6486232627 1005857 SRX26812022 SRS23296671 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.95941 0.96004 0.10323 0.10191 0.65451 0.6532 0.46396 0.46398 101 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34194 34194 SRR31443230 SRX26812021 SRS23296670 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 2   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 2 srrm4[y712] mutant replicate 2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut2.pass2Aligned.sortedByCoord.out.bam bam 20256127500.0 101792067.0 25938 mut2.pass2Aligned.sortedByCoord.out.bam 0:100.05 1:100.00 A:5435798119;C:4683997479;G:4650293108;T:5485187428;N:851366 100 100     5435798119 4683997479 4650293108 5485187428 851366 SRX26812021 SRS23296670 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.96008 0.96049 0.10232 0.10156 0.66072 0.65932 0.4668 0.46817 95 95 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34195 34195 SRR31443231 SRX26812020 SRS23296669 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 2   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 2 srrm4[y712] wild type replicate 2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt2.pass2Aligned.sortedByCoord.out.bam bam 22698373371.0 113599687.0 25938 wt2.pass2Aligned.sortedByCoord.out.bam 0:100.18 1:100.12 A:6063922145;C:5275724786;G:5212055837;T:6145709475;N:961128 100 100     6063922145 5275724786 5212055837 6145709475 961128 SRX26812020 SRS23296669 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.96129 0.96063 0.1003 0.09861 0.65744 0.65748 0.46167 0.46817 98 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34196 34196 SRR31443232 SRX26812019 SRS23296667 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 1   strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 1 srrm4[y712] mutant replicate 1 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut.pass2Aligned.sortedByCoord.out.bam bam 11282501509.0 56702666.0 25938 mut.pass2Aligned.sortedByCoord.out.bam 0:99.65 1:99.55 A:2764745971;C:2868447715;G:2856237429;T:2792914545;N:155849 99 99     2764745971 2868447715 2856237429 2792914545 155849 SRX26812019 SRS23296667 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34197 34197 SRR31443233 SRX26812018 SRS23296668 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 1   strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 1 srrm4[y712] wild type replicate 1 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt.pass2Aligned.sortedByCoord.out.bam bam 16346812838.0 82104499.0 25938 wt.pass2Aligned.sortedByCoord.out.bam 0:99.65 1:99.56 A:3996717287;C:4167381503;G:4130586142;T:4051899914;N:227992 99 99     3996717287 4167381503 4130586142 4051899914 227992 SRX26812018 SRS23296668 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.97776 0.97907 0.04095 0.04006 0.6702 0.67034 0.46611 0.46144 99 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34945 34945 SRR32472665 SRX27787001 SRS24165038 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched mtmr5 knockout biol rep4 GSM8811137   source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing Brain enriched mtmr5 knockout biol rep4 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:mtmr5 knockout GSM8811137 GSM8811137: Brain enriched mtmr5 knockout biol rep4; Danio rerio; RNA Seq GSM8811137 r1 GSM8811137 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_KO_4_S45_L002_R1_001.fastq.gz mtmr5_KO_4_S45_L002_R2_001.fastq.gz fastq fastq 10453259182.0 34613441.0 GSM8811137 r1 0:151 1:151 A:3266219433;C:1966251945;G:2032163425;T:3188611188;N:13191 151 151     3266219433 1966251945 2032163425 3188611188 13191 SRX27787001 SRS24165038 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34946 34946 SRR32472666 SRX27787000 SRS24165036 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched mtmr5 knockout biol rep3 GSM8811136   source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing Brain enriched mtmr5 knockout biol rep3 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:mtmr5 knockout GSM8811136 GSM8811136: Brain enriched mtmr5 knockout biol rep3; Danio rerio; RNA Seq GSM8811136 r1 GSM8811136 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_KO_3_S43_L002_R1_001.fastq.gz mtmr5_KO_3_S43_L002_R2_001.fastq.gz fastq fastq 12084666202.0 40015451.0 GSM8811136 r1 0:151 1:151 A:3753711310;C:2294198185;G:2375272418;T:3661468451;N:15838 151 151     3753711310 2294198185 2375272418 3661468451 15838 SRX27787000 SRS24165036 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34947 34947 SRR32472667 SRX27786999 SRS24165037 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched mtmr5 knockout biol rep2 GSM8811135   source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing Brain enriched mtmr5 knockout biol rep2 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:mtmr5 knockout GSM8811135 GSM8811135: Brain enriched mtmr5 knockout biol rep2; Danio rerio; RNA Seq GSM8811135 r1 GSM8811135 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_KO_2_S41_L002_R1_001.fastq.gz mtmr5_KO_2_S41_L002_R2_001.fastq.gz fastq fastq 11376848568.0 37671684.0 GSM8811135 r1 0:151 1:151 A:3528535891;C:2164674917;G:2231865046;T:3451757695;N:15019 151 151     3528535891 2164674917 2231865046 3451757695 15019 SRX27786999 SRS24165037 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34948 34948 SRR32472668 SRX27786998 SRS24165034 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched mtmr5 knockout biol rep1 GSM8811134   source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing Brain enriched mtmr5 knockout biol rep1 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:mtmr5 knockout GSM8811134 GSM8811134: Brain enriched mtmr5 knockout biol rep1; Danio rerio; RNA Seq GSM8811134 r1 GSM8811134 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_KO_1_S39_L002_R1_001.fastq.gz mtmr5_KO_1_S39_L002_R2_001.fastq.gz fastq fastq 10620109350.0 35165925.0 GSM8811134 r1 0:151 1:151 A:3306163050;C:2008249825;G:2075153541;T:3230528981;N:13953 151 151     3306163050 2008249825 2075153541 3230528981 13953 SRX27786998 SRS24165034 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34949 34949 SRR32472669 SRX27786997 SRS24165033 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched wild type biol rep4 GSM8811133   source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing Brain enriched wild type biol rep4 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:wild type GSM8811133 GSM8811133: Brain enriched wild type biol rep4; Danio rerio; RNA Seq GSM8811133 r1 GSM8811133 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_WT_4_S44_L002_R1_001.fastq.gz mtmr5_WT_4_S44_L002_R2_001.fastq.gz fastq fastq 12990872770.0 43016135.0 GSM8811133 r1 0:151 1:151 A:3923529419;C:2571621367;G:2649969483;T:3845735356;N:17145 151 151     3923529419 2571621367 2649969483 3845735356 17145 SRX27786997 SRS24165033 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning 2 0.89808 0.89653 0.27845 0.2761 0.74479 0.74412 0.52081 0.52503 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34950 34950 SRR32472670 SRX27786996 SRS24165032 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched wild type biol rep3 GSM8811132   source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing Brain enriched wild type biol rep3 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:wild type GSM8811132 GSM8811132: Brain enriched wild type biol rep3; Danio rerio; RNA Seq GSM8811132 r1 GSM8811132 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_WT_3_S42_L002_R1_001.fastq.gz mtmr5_WT_3_S42_L002_R2_001.fastq.gz fastq fastq 11980025618.0 39668959.0 GSM8811132 r1 0:151 1:151 A:3620876130;C:2376508941;G:2435934723;T:3546690015;N:15809 151 151     3620876130 2376508941 2435934723 3546690015 15809 SRX27786996 SRS24165032 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34951 34951 SRR32472671 SRX27786995 SRS24165035 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched wild type biol rep2 GSM8811131   source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing Brain enriched wild type biol rep2 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:wild type GSM8811131 GSM8811131: Brain enriched wild type biol rep2; Danio rerio; RNA Seq GSM8811131 r1 GSM8811131 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_WT_2_S40_L002_R1_001.fastq.gz mtmr5_WT_2_S40_L002_R2_001.fastq.gz fastq fastq 12148102812.0 40225506.0 GSM8811131 r1 0:151 1:151 A:3574846721;C:2501278590;G:2563116243;T:3508845082;N:16176 151 151     3574846721 2501278590 2563116243 3508845082 16176 SRX27786995 SRS24165035 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34952 34952 SRR32472672 SRX27786994 SRS24165031 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched wild type biol rep1 GSM8811130   source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing Brain enriched wild type biol rep1 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:wild type GSM8811130 GSM8811130: Brain enriched wild type biol rep1; Danio rerio; RNA Seq GSM8811130 r1 GSM8811130 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_WT_1_S38_L002_R1_001.fastq.gz mtmr5_WT_1_S38_L002_R2_001.fastq.gz fastq fastq 12280050236.0 40662418.0 GSM8811130 r1 0:151 1:151 A:3666524090;C:2479893988;G:2540363922;T:3593251867;N:16369 151 151     3666524090 2479893988 2540363922 3593251867 16369 SRX27786994 SRS24165031 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning 2 0.91363 0.9138 0.2442 0.24267 0.72232 0.72123 0.47864 0.53039 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head 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
56512 56512 SRR10988549 SRX7649999 SRS6079496 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 sib3 GSM4289907   source name:head|tissue:Head|age:2dpf head 2d rw440 sib3 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf GSM4289907 GSM4289907: head 2d rw440 sib3; Danio rerio; RNA Seq GSM4289907   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289907 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_sib3_R2.fastq.gz 2d_rw440_sib3_R1.fastq.gz fastq fastq 3140682329.0 10457484.0 GSM4289907 r1 0:150.21 1:150.12 A:760684292;C:777389008;G:783922642;T:818121129;N:565258 150 150     760684292 777389008 783922642 818121129 565258 SRX7649999 SRS6079496 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93527 0.95251 0.03293 0.02826 0.72032 0.73669 0.4787 0.47899 150 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56513 56513 SRR10988548 SRX7649998 SRS6079495 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 sib2 GSM4289906   source name:head|tissue:Head|age:2dpf head 2d rw440 sib2 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf GSM4289906 GSM4289906: head 2d rw440 sib2; Danio rerio; RNA Seq GSM4289906   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289906 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_sib2_R1.fastq.gz 2d_rw440_sib2_R2.fastq.gz fastq fastq 3194598681.0 10634398.0 GSM4289906 r1 0:150.24 1:150.17 A:771547062;C:789590364;G:796831526;T:835985747;N:643982 150 150     771547062 789590364 796831526 835985747 643982 SRX7649998 SRS6079495 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93377 0.95416 0.02628 0.02182 0.72989 0.74805 0.46631 0.47654 149 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56514 56514 SRR10988547 SRX7649997 SRS6079494 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 sib1 GSM4289905   source name:head|tissue:Head|age:2dpf head 2d rw440 sib1 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf GSM4289905 GSM4289905: head 2d rw440 sib1; Danio rerio; RNA Seq GSM4289905   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289905 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_sib1_R1.fastq.gz 2d_rw440_sib1_R2.fastq.gz fastq fastq 2654979688.0 8840507.0 GSM4289905 r1 0:150.19 1:150.13 A:624000299;C:675145222;G:678635011;T:676731946;N:467210 150 150     624000299 675145222 678635011 676731946 467210 SRX7649997 SRS6079494 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.9317 0.94861 0.06364 0.05753 0.72811 0.75055 0.50771 0.52256 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56515 56515 SRR10988546 SRX7649996 SRS6079493 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 mut3 GSM4289904   source name:head|tissue:Head|age:2dpf / head 2d rw440 mut3 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf / GSM4289904 GSM4289904: head 2d rw440 mut3; Danio rerio; RNA Seq GSM4289904   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289904 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_mut3_R1.fastq.gz 2d_rw440_mut3_R2.fastq.gz fastq fastq 3282506507.0 10958106.0 GSM4289904 r1 0:149.81 1:149.74 A:781014809;C:816143245;G:824711112;T:858035111;N:2602230 149 149     781014809 816143245 824711112 858035111 2602230 SRX7649996 SRS6079493 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93293 0.95901 0.02641 0.023 0.74408 0.76449 0.48032 0.475 151 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56516 56516 SRR10988545 SRX7649995 SRS6079492 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 mut2 GSM4289903   source name:head|tissue:Head|age:2dpf / head 2d rw440 mut2 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf / GSM4289903 GSM4289903: head 2d rw440 mut2; Danio rerio; RNA Seq GSM4289903   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289903 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_mut2_R2.fastq.gz 2d_rw440_mut2_R1.fastq.gz fastq fastq 2673347852.0 8908620.0 GSM4289903 r1 0:150.07 1:150.01 A:641733072;C:667262119;G:672992510;T:690242042;N:1118109 150 150     641733072 667262119 672992510 690242042 1118109 SRX7649995 SRS6079492 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93754 0.95755 0.03962 0.0352 0.72234 0.73963 0.47668 0.49072 151 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56517 56517 SRR10988544 SRX7649994 SRS6079491 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 mut1 GSM4289902   source name:head|tissue:Head|age:2dpf / head 2d rw440 mut1 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf / GSM4289902 GSM4289902: head 2d rw440 mut1; Danio rerio; RNA Seq GSM4289902   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289902 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_mut1_R1.fastq.gz 2d_rw440_mut1_R2.fastq.gz fastq fastq 2609801785.0 8695280.0 GSM4289902 r1 0:150.10 1:150.04 A:629026157;C:649393814;G:654616712;T:676204104;N:560998 150 150     629026157 649393814 654616712 676204104 560998 SRX7649994 SRS6079491 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93478 0.95296 0.02959 0.0259 0.72458 0.74209 0.4765 0.47804 151 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head 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
62931 62931 SRR13447020 SRX9860256 SRS8040687 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 14 3 wpi sc 2 GSM5023609   source name:21 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:21 xxx post injury Z 14 3 wpi sc 2 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 21 xxx post injury dpi whole bulk spinal cord Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:bulk spinal cord|timepoint:21 xxx post injury GSM5023609 GSM5023609: Z 14 3 wpi sc 2; Danio rerio; RNA Seq GSM5023609   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023609 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_GGTTTCG.fq.gz fastq 1344754850.0 26895097.0 GSM5023609 r1 0:50 1:0 A:368949168;C:303436511;G:303863091;T:368250015;N:256065 50 0     368949168 303436511 303863091 368250015 256065 SRX9860256 SRS8040687 SRA1184552 GEO Developmental Biology, Washington University 1 0.90723   0.15091   0.70701   0.50468   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62932 62932 SRR13447019 SRX9860255 SRS8040686 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 10 3 wpi sc 1 GSM5023608   source name:21 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:21 xxx post injury Z 10 3 wpi sc 1 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 21 xxx post injury dpi whole bulk spinal cord Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:bulk spinal cord|timepoint:21 xxx post injury GSM5023608 GSM5023608: Z 10 3 wpi sc 1; Danio rerio; RNA Seq GSM5023608   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023608 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_GACCGAA.fq.gz fastq 1479770950.0 29595419.0 GSM5023608 r1 0:50 1:0 A:405566463;C:336370965;G:334352978;T:403198702;N:281842 50 0     405566463 336370965 334352978 403198702 281842 SRX9860255 SRS8040686 SRA1184552 GEO Developmental Biology, Washington University 1 0.90956   0.14428   0.70666   0.40811   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62933 62933 SRR13447018 SRX9860254 SRS8040685 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 13 10 dpi sc 2 GSM5023607   source name:10 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:10 xxx post injury Z 13 10 dpi sc 2 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 10 xxx post injury dpi whole bulk spinal cord Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:bulk spinal cord|timepoint:10 xxx post injury GSM5023607 GSM5023607: Z 13 10 dpi sc 2; Danio rerio; RNA Seq GSM5023607   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023607 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_TTACCGT.fq.gz fastq 2001230650.0 40024613.0 GSM5023607 r1 0:50 1:0 A:563937717;C:433011935;G:427243197;T:576659283;N:378518 50 0     563937717 433011935 427243197 576659283 378518 SRX9860254 SRS8040685 SRA1184552 GEO Developmental Biology, Washington University 1 0.88738   0.25515   0.74576   0.61121   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62934 62934 SRR13447017 SRX9860253 SRS8040684 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 9 10 dpi sc 1 GSM5023606   source name:10 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:10 xxx post injury Z 9 10 dpi sc 1 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 10 xxx post injury dpi whole bulk spinal cord Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:bulk spinal cord|timepoint:10 xxx post injury GSM5023606 GSM5023606: Z 9 10 dpi sc 1; Danio rerio; RNA Seq GSM5023606   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023606 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_TAGGATG.fq.gz fastq 1228530350.0 24570607.0 GSM5023606 r1 0:50 1:0 A:336797190;C:276687423;G:274112310;T:340700127;N:233300 50 0     336797190 276687423 274112310 340700127 233300 SRX9860253 SRS8040684 SRA1184552 GEO Developmental Biology, Washington University 1 0.90494   0.17991   0.69789   0.43663   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62935 62935 SRR13447016 SRX9860252 SRS8040683 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 12 5 dpi sc 2 GSM5023605   source name:5 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:5 xxx post injury Z 12 5 dpi sc 2 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 5 xxx post injury dpi whole bulk spinal cord Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:bulk spinal cord|timepoint:5 xxx post injury GSM5023605 GSM5023605: Z 12 5 dpi sc 2; Danio rerio; RNA Seq GSM5023605   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023605 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_CGCCGTA.fq.gz fastq 1304617300.0 26092346.0 GSM5023605 r1 0:50 1:0 A:354720856;C:300934683;G:299416035;T:349298501;N:247225 50 0     354720856 300934683 299416035 349298501 247225 SRX9860252 SRS8040683 SRA1184552 GEO Developmental Biology, Washington University 1 0.91217   0.12965   0.69609   0.45367   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62936 62936 SRR13447015 SRX9860251 SRS8040682 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 8 5 dpi sc 1 GSM5023604   source name:5 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:5 xxx post injury Z 8 5 dpi sc 1 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 5 xxx post injury dpi whole bulk spinal cord Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:bulk spinal cord|timepoint:5 xxx post injury GSM5023604 GSM5023604: Z 8 5 dpi sc 1; Danio rerio; RNA Seq GSM5023604   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023604 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_CATACTG.fq.gz fastq 1396287400.0 27925748.0 GSM5023604 r1 0:50 1:0 A:377321251;C:319668467;G:314347283;T:384684913;N:265486 50 0     377321251 319668467 314347283 384684913 265486 SRX9860251 SRS8040682 SRA1184552 GEO Developmental Biology, Washington University 1 0.91125   0.14506   0.69777   0.4557   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62937 62937 SRR13447014 SRX9860250 SRS8040681 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 11 uninjured sc 2 GSM5023603   source name:Bulk uninjured spinal cord|tissue:bulk spinal cord|timepoint:Uninjured Z 11 uninjured sc 2 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 Bulk uninjured spinal cord Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:bulk spinal cord|timepoint:Uninjured GSM5023603 GSM5023603: Z 11 uninjured sc 2; Danio rerio; RNA Seq GSM5023603   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023603 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_CGTGATA.fq.gz fastq 1422401500.0 28448030.0 GSM5023603 r1 0:50 1:0 A:383424800;C:325837613;G:322858241;T:390009650;N:271196 50 0     383424800 325837613 322858241 390009650 271196 SRX9860250 SRS8040681 SRA1184552 GEO Developmental Biology, Washington University 1 0.918   0.1183   0.7163   0.50669   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62938 62938 SRR13447013 SRX9860249 SRS8040680 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 7 uninjured sc 1 GSM5023602   source name:Bulk uninjured spinal cord|tissue:bulk spinal cord|timepoint:Uninjured Z 7 uninjured sc 1 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 Bulk uninjured spinal cord Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:bulk spinal cord|timepoint:Uninjured GSM5023602 GSM5023602: Z 7 uninjured sc 1; Danio rerio; RNA Seq GSM5023602   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023602 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_CCCGCTA.fq.gz fastq 1274023900.0 25480478.0 GSM5023602 r1 0:50 1:0 A:330443270;C:305732881;G:301431401;T:336172878;N:243470 50 0     330443270 305732881 301431401 336172878 243470 SRX9860249 SRS8040680 SRA1184552 GEO Developmental Biology, Washington University 1 0.92713   0.09501   0.71776   0.49328   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62939 62939 SRR13447012 SRX9860248 SRS8040679 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 3 gp rp rna 1 GSM5023601   source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury Z 3 gp rp rna 1 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 FACS sorted ctgfa:mCherry;gfap:EGFP cells Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury GSM5023601 GSM5023601: Z 3 gp rp rna 1; Danio rerio; RNA Seq GSM5023601   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023601 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_ATAGGCT.fq.gz fastq 1480993150.0 29619863.0 GSM5023601 r1 0:50 1:0 A:407241408;C:335585510;G:332782981;T:405104683;N:278568 50 0     407241408 335585510 332782981 405104683 278568 SRX9860248 SRS8040679 SRA1184552 GEO Developmental Biology, Washington University 1 0.90012   0.13909   0.75684   0.59867   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62940 62940 SRR13447011 SRX9860247 SRS8040678 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 18 gp rp 3 GSM5023600   source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury Z 18 gp rp 3 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 FACS sorted ctgfa:mCherry;gfap:EGFP cells Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury GSM5023600 GSM5023600: Z 18 gp rp 3; Danio rerio; RNA Seq GSM5023600   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023600 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_AATGACT.fq.gz fastq 1583531750.0 31670635.0 GSM5023600 r1 0:50 1:0 A:429031314;C:366679713;G:363462738;T:424058514;N:299471 50 0     429031314 366679713 363462738 424058514 299471 SRX9860247 SRS8040678 SRA1184552 GEO Developmental Biology, Washington University 1 0.90969   0.12671   0.7458   0.57895   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
62941 62941 SRR13447010 SRX9860246 SRS8040677 SRP301982 PRJNA692493 Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq] GSE164943 Transcriptome Analysis mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue. parent bioproject:PRJNA692492 pubmed:33609461   Z 15 gp rp 1 GSM5023599   source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury Z 15 gp rp 1 Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11 FACS sorted ctgfa:mCherry;gfap:EGFP cells Adult zebrafish were subjected to complete spinal cord transection or sham injured control. For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads   tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury GSM5023599 GSM5023599: Z 15 gp rp 1; Danio rerio; RNA Seq GSM5023599   1 For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads GEO Accession:GSM5023599 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP301982     run_2941_s_5_withindex_sequence.txt_TTCTTCG.fq.gz fastq 1324698650.0 26493973.0 GSM5023599 r1 0:50 1:0 A:361437407;C:301526323;G:300125135;T:361356767;N:253018 50 0     361437407 301526323 300125135 361356767 253018 SRX9860246 SRS8040677 SRA1184552 GEO Developmental Biology, Washington University 1 0.90938   0.14229   0.70869   0.50563   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2021-01-15 Adult Adult Spinal Cord Nervous System
65793 65793 SRR15626575 SRX11923642 SRS9937160 SRP334272 PRJNA758088 Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury GSE182868 Transcriptome Analysis The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol. parent bioproject:PRJNA758278 pubmed:34876587   W6 C5 GSM5538904   source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury W6 C5 Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample. spinal cord   Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury GSM5538904 GSM5538904: W6 C5; Danio rerio; RNA Seq GSM5538904   1 Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5538904 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP334272   loader:fastq load.py W6_C5_1.fq.gz W6_C5_2.fq.gz fastq fastq 11548053600.0 38493512.0 GSM5538904 r1 0:150 1:150 A:3284639772;C:2417614008;G:2424125351;T:3421247186;N:427283 150 150     3284639772 2417614008 2424125351 3421247186 427283 SRX11923642 SRS9937160 SRA1284220 GEO Neuroscience, School of Medcine, Tongji University, 42508444-9 2 0.92424 0.91753 0.09206 0.08921 0.73817 0.75006 0.48669 0.46123 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2021-08-26 Undetermined Adult Spinal Cord Nervous System
65794 65794 SRR15626574 SRX11923641 SRS9937158 SRP334272 PRJNA758088 Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury GSE182868 Transcriptome Analysis The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol. parent bioproject:PRJNA758278 pubmed:34876587   W6 C3 GSM5538903   source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury W6 C3 Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample. spinal cord   Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury GSM5538903 GSM5538903: W6 C3; Danio rerio; RNA Seq GSM5538903   1 Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5538903 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP334272   loader:fastq load.py W6_C3_1.fq.gz W6_C3_2.fq.gz fastq fastq 8675036411.0 29294039.0 GSM5538903 r1   A:2490417531;C:1754549667;G:1762976045;T:2666940038;N:153130         2490417531 1754549667 1762976045 2666940038 153130 SRX11923641 SRS9937158 SRA1284220 GEO Neuroscience, School of Medcine, Tongji University, 42508444-9 2 0.77214 0.76518 0.16042 0.15604 0.72425 0.74251 0.47844 0.47263 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2021-08-26 Undetermined Adult Spinal Cord Nervous System
65795 65795 SRR15626573 SRX11923640 SRS9937159 SRP334272 PRJNA758088 Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury GSE182868 Transcriptome Analysis The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol. parent bioproject:PRJNA758278 pubmed:34876587   W6 C2 GSM5538902   source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury W6 C2 Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample. spinal cord   Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury GSM5538902 GSM5538902: W6 C2; Danio rerio; RNA Seq GSM5538902   1 Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5538902 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP334272   loader:fastq load.py W6_C2_1.fq.gz W6_C2_2.fq.gz fastq fastq 10539241978.0 35799607.0 GSM5538902 r1   A:2981919265;C:2108326349;G:2140188676;T:3307713377;N:1094311         2981919265 2108326349 2140188676 3307713377 1094311 SRX11923640 SRS9937159 SRA1284220 GEO Neuroscience, School of Medcine, Tongji University, 42508444-9 2 0.79298 0.77869 0.15756 0.14594 0.71504 0.73527 0.52219 0.3777 126 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2021-08-26 Undetermined Adult Spinal Cord Nervous System
65796 65796 SRR15626572 SRX11923639 SRS9937157 SRP334272 PRJNA758088 Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury GSE182868 Transcriptome Analysis The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol. parent bioproject:PRJNA758278 pubmed:34876587   W6 C1 GSM5538901   source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury W6 C1 Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample. spinal cord   Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury GSM5538901 GSM5538901: W6 C1; Danio rerio; RNA Seq GSM5538901   1 Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5538901 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP334272   loader:fastq load.py W6_C1_1.fq.gz W6_C1_2.fq.gz fastq fastq 10943049099.0 37073140.0 GSM5538901 r1   A:3130283377;C:2198486300;G:2220073292;T:3393075128;N:1131002         3130283377 2198486300 2220073292 3393075128 1131002 SRX11923639 SRS9937157 SRA1284220 GEO Neuroscience, School of Medcine, Tongji University, 42508444-9 2 0.80382 0.80796 0.16342 0.16071 0.72275 0.73456 0.49635 0.49821 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2021-08-26 Undetermined Adult Spinal Cord Nervous System
65797 65797 SRR15626571 SRX11923638 SRS9937156 SRP334272 PRJNA758088 Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury GSE182868 Transcriptome Analysis The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol. parent bioproject:PRJNA758278 pubmed:34876587   W6 R5 GSM5538900   source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury W6 R5 Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample. spinal cord   Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury GSM5538900 GSM5538900: W6 R5; Danio rerio; RNA Seq GSM5538900   1 Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5538900 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP334272   loader:fastq load.py W6_R5_1.fq.gz W6_R5_2.fq.gz fastq fastq 12204896100.0 40682987.0 GSM5538900 r1 0:150 1:150 A:3461249396;C:2529425680;G:2571904738;T:3640345896;N:1970390 150 150     3461249396 2529425680 2571904738 3640345896 1970390 SRX11923638 SRS9937156 SRA1284220 GEO Neuroscience, School of Medcine, Tongji University, 42508444-9 2 0.91134 0.91584 0.10821 0.10746 0.73588 0.75207 0.52657 0.48765 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2021-08-26 Undetermined Adult Spinal Cord Nervous System
65798 65798 SRR15626570 SRX11923637 SRS9937155 SRP334272 PRJNA758088 Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury GSE182868 Transcriptome Analysis The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol. parent bioproject:PRJNA758278 pubmed:34876587   W6 R4 GSM5538899   source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury W6 R4 Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample. spinal cord   Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury GSM5538899 GSM5538899: W6 R4; Danio rerio; RNA Seq GSM5538899   1 Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5538899 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP334272   loader:fastq load.py W6_R4_1.fq.gz W6_R4_2.fq.gz fastq fastq 11563962300.0 38546541.0 GSM5538899 r1 0:150 1:150 A:3303789178;C:2399710240;G:2415791330;T:3443551642;N:1119910 150 150     3303789178 2399710240 2415791330 3443551642 1119910 SRX11923637 SRS9937155 SRA1284220 GEO Neuroscience, School of Medcine, Tongji University, 42508444-9 2 0.91143 0.90985 0.11486 0.11393 0.73825 0.74533 0.54532 0.52817 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2021-08-26 Undetermined Adult Spinal Cord Nervous System
65799 65799 SRR15626569 SRX11923636 SRS9937154 SRP334272 PRJNA758088 Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury GSE182868 Transcriptome Analysis The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol. parent bioproject:PRJNA758278 pubmed:34876587   W6 R3 GSM5538898   source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury W6 R3 Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample. spinal cord   Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury GSM5538898 GSM5538898: W6 R3; Danio rerio; RNA Seq GSM5538898   1 Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5538898 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP334272   loader:fastq load.py W6_R3_1.fq.gz W6_R3_2.fq.gz fastq fastq 10585954542.0 35816604.0 GSM5538898 r1   A:3037575766;C:2127628123;G:2139476709;T:3281099271;N:174673         3037575766 2127628123 2139476709 3281099271 174673 SRX11923636 SRS9937154 SRA1284220 GEO Neuroscience, School of Medcine, Tongji University, 42508444-9 2 0.85058 0.85296 0.1621 0.15714 0.71713 0.73582 0.52255 0.50069 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2021-08-26 Undetermined Adult Spinal Cord 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");;