{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"bulk\" and tissue_curation = \"Brain\"", "rows": [[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", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. 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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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "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, null, null, 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", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "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, null, null, 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", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "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, null, null, 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", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "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, null, null, 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", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "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, null, null, 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", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X9 tp53mut control", "GSM7774465", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X8 tp53mut control", "GSM7774464", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X7 tp53mut control", "GSM7774463", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X6 tp53het tumor", "GSM7774462", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X5 tp53het tumor", "GSM7774461", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X4 tp53het tumor", "GSM7774460", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X3 tp53mut tumor", "GSM7774459", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Larval", "Larval", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X2 tp53mut tumor", "GSM7774458", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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.", null, "pubmed:39078737", null, "19521X1 tp53mut tumor", "GSM7774457", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP459779", null, "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, null, null, 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", null, "United States", "2023-09-11", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii  PI3KCAH1047R  mScarlet tumor negative control brain 2", "GSM7866394", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 1894557984, 1627945034, 1550203852, 2009224463, 16765, "SRX22238470", "SRS19292731", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94543, null, 0.14646, null, 0.68883, null, 0.49451, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii  PI3KCAH1047R  mScarlet tumor negative control brain 1", "GSM7866393", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2099360211, 1783653297, 1717681461, 2239858766, 18594, "SRX22238469", "SRS19292730", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93984, null, 0.1663, null, 0.69033, null, 0.484, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R  GFP tumor negative control brain", "GSM7866392", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2650336113, 2354113843, 2276252979, 2884188285, 23500, "SRX22238468", "SRS19292729", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94271, null, 0.10831, null, 0.68527, null, 0.50207, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii  PI3KCAH1047R  mScarlet tumor positive whole brain 3", "GSM7866391", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2627522717, 2223655583, 2134761894, 2810751194, 22782, "SRX22238467", "SRS19292728", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.92543, null, 0.1876, null, 0.67308, null, 0.4886, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii  PI3KCAH1047R  mScarlet tumor positive whole brain 2", "GSM7866390", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2093456023, 1792947580, 1718784421, 2234389453, 18384, "SRX22238466", "SRS19292727", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93807, null, 0.14978, null, 0.68854, null, 0.47786, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii  PI3KCAH1047R  mScarlet tumor positive whole brain 1", "GSM7866389", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2217465507, 1940028683, 1857031218, 2388930530, 19590, "SRX22238465", "SRS19292726", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94596, null, 0.12916, null, 0.68619, null, 0.4957, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R  GFP tumor positive whole brain 3", "GSM7866388", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2040241047, 1721563382, 1666400346, 2180961056, 17619, "SRX22238464", "SRS19292725", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93555, null, 0.16895, null, 0.68199, null, 0.50032, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R  GFP tumor positive whole brain 2", "GSM7866387", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2223763293, 1944013929, 1869828652, 2408947564, 19901, "SRX22238463", "SRS19292724", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94943, null, 0.11539, null, 0.68428, null, 0.51019, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R  GFP tumor positive whole brain 1", "GSM7866386", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 1143856405, 993993009, 951829931, 1236519669, 10039, "SRX22238462", "SRS19292723", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94443, null, 0.13057, null, 0.68503, null, 0.50149, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [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.", null, "pubmed:29686887", null, "PCB126 BRAIN4 RNA Seq", "GSM2792798", null, "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.", null, "treatment:PCB126|life history stage:Adult", "GSM2792798", "GSM2792798: PCB126 BRAIN4 RNA Seq; Danio rerio; RNA Seq", "GSM2792798", null, "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", null, "SRP118819", null, null, "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, null, null, 389260936, 298336750, 285290157, 402727589, 13076, "SRX3214272", "SRS2539011", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.90102, null, 0.20673, null, 0.69152, null, 0.51941, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:29686887", null, "PCB126 BRAIN3 RNA Seq", "GSM2792797", null, "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.", null, "treatment:PCB126|life history stage:Adult", "GSM2792797", "GSM2792797: PCB126 BRAIN3 RNA Seq; Danio rerio; RNA Seq", "GSM2792797", null, "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", null, "SRP118819", null, null, "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, null, null, 434098364, 333114785, 318943720, 448043305, 13854, "SRX3214271", "SRS2539012", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.88591, null, 0.19161, null, 0.67967, null, 0.53267, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:29686887", null, "PCB126 BRAIN2 RNA Seq", "GSM2792796", null, "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.", null, "treatment:PCB126|life history stage:Adult", "GSM2792796", "GSM2792796: PCB126 BRAIN2 RNA Seq; Danio rerio; RNA Seq", "GSM2792796", null, "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", null, "SRP118819", null, null, "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, null, null, 419506485, 327077186, 314622527, 431420803, 14275, "SRX3214270", "SRS2539009", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.89327, null, 0.18282, null, 0.68777, null, 0.53375, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:29686887", null, "PCB126 BRAIN1 RNA Seq", "GSM2792795", null, "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.", null, "treatment:PCB126|life history stage:Adult", "GSM2792795", "GSM2792795: PCB126 BRAIN1 RNA Seq; Danio rerio; RNA Seq", "GSM2792795", null, "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", null, "SRP118819", null, null, "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, null, null, 425532690, 346041208, 332010797, 436640179, 14702, "SRX3214269", "SRS2539010", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.8846, null, 0.14495, null, 0.67142, null, 0.51907, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:29686887", null, "CONTROL BRAIN4 RNA Seq", "GSM2792794", null, "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.", null, "treatment:DMSO|life history stage:Adult", "GSM2792794", "GSM2792794: CONTROL BRAIN4 RNA Seq; Danio rerio; RNA Seq", "GSM2792794", null, "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", null, "SRP118819", null, null, "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, null, null, 408992269, 323726908, 309480781, 421041726, 13851, "SRX3214268", "SRS2539008", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.89686, null, 0.19559, null, 0.69871, null, 0.50956, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:29686887", null, "CONTROL BRAIN3 RNA Seq", "GSM2792793", null, "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.", null, "treatment:DMSO|life history stage:Adult", "GSM2792793", "GSM2792793: CONTROL BRAIN3 RNA Seq; Danio rerio; RNA Seq", "GSM2792793", null, "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", null, "SRP118819", null, null, "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, null, null, 452040960, 360441413, 344970351, 466800984, 15202, "SRX3214267", "SRS2539124", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.89974, null, 0.19642, null, 0.6896, null, 0.49428, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:29686887", null, "CONTROL BRAIN2 RNA Seq", "GSM2792792", null, "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.", null, "treatment:DMSO|life history stage:Adult", "GSM2792792", "GSM2792792: CONTROL BRAIN2 RNA Seq; Danio rerio; RNA Seq", "GSM2792792", null, "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", null, "SRP118819", null, null, "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, null, null, 480819797, 388942062, 374434527, 495998198, 16094, "SRX3214266", "SRS2539123", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.91021, null, 0.19053, null, 0.68603, null, 0.4987, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Brain", "Nervous System"], [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.", null, "pubmed:29686887", null, "CONTROL BRAIN1 RNA Seq", "GSM2792791", null, "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.", null, "treatment:DMSO|life history stage:Adult", "GSM2792791", "GSM2792791: CONTROL BRAIN1 RNA Seq; Danio rerio; RNA Seq", "GSM2792791", null, "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", null, "SRP118819", null, null, "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, null, null, 476861764, 381757171, 366051176, 490460394, 16172, "SRX3214265", "SRS2539120", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.90508, null, 0.18823, null, 0.69607, null, 0.51563, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Brain", "Nervous System"], [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", null, "AB7155", "GSM3963895", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 331549647, 254056286, 280458785, 273550294, 109255, "SRX6581798", "SRS5147496", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.90535, null, 0.17532, null, 0.87803, null, 0.67683, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "AB7154", "GSM3963894", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 337010566, 261723350, 290674768, 271864761, 111164, "SRX6581797", "SRS5147495", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.89031, null, 0.18199, null, 0.88154, null, 0.67975, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "AB7153", "GSM3963893", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 320167297, 243538818, 266263775, 258739754, 101386, "SRX6581796", "SRS5147494", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.89179, null, 0.12861, null, 0.87259, null, 0.63828, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "AB5657", "GSM3963892", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 89857088, 69771659, 81302142, 90395650, 6010, "SRX6581795", "SRS5147493", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.88981, null, 0.33973, null, 0.93507, null, 0.6341, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "AB5657", "GSM3963892", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 223319161, 173475726, 194239433, 205842249, 31548, "SRX6581795", "SRS5147493", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.8909, null, 0.30223, null, 0.91802, null, 0.65318, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "AB3014", "GSM3963891", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 546306466, 392206824, 436944803, 478712291, 27346, "SRX6581794", "SRS5147492", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.90278, null, 0.4347, null, 0.88925, null, 0.64871, null, 66, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "pubmed:32859696", null, "GH6", "GSM4002525", null, "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", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GSM4002525", "GSM4002525: GH6; Danio rerio; RNA Seq", "GSM4002525", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "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, null, null, 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", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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", null, "pubmed:32859696", null, "GH5", "GSM4002524", null, "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", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GSM4002524", "GSM4002524: GH5; Danio rerio; RNA Seq", "GSM4002524", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "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, null, null, 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", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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", null, "pubmed:32859696", null, "GH4", "GSM4002523", null, "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", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf dj 1  / ", "GSM4002523", "GSM4002523: GH4; Danio rerio; RNA Seq", "GSM4002523", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002523", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "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, null, null, 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", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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", null, "pubmed:32859696", null, "GH3", "GSM4002522", null, "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", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf type", "GSM4002522", "GSM4002522: GH3; Danio rerio; RNA Seq", "GSM4002522", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002522", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "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, null, null, 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", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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", null, "pubmed:32859696", null, "GH2", "GSM4002521", null, "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", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf type", "GSM4002521", "GSM4002521: GH2; Danio rerio; RNA Seq", "GSM4002521", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002521", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "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, null, null, 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", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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", null, "pubmed:32859696", null, "GH1", "GSM4002520", null, "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", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", null, "strain:LWT|tissue:Brain|age:12 wpf type", "GSM4002520", "GSM4002520: GH1; Danio rerio; RNA Seq", "GSM4002520", null, "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\u00ae PolyA mRNA Magnetic Isolation Module following manufacturers instructions.", "GEO Accession:GSM4002520", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP217245", null, null, "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, null, null, 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", null, "United Kingdom", "2019-08-01", "Juvenile", "Juvenile", "Brain", "Nervous System"], [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", null, "pubmed:34054419;pubmed:35204047", null, "injured telencephalic hemisphere 3", "GSM4887529", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:injury", "GSM4887529", "GSM4887529: injured telencephalic hemisphere 3; Danio rerio; RNA Seq", "GSM4887529", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 333355914, 282050013, 361225960, 448164522, 0, "SRX9450941", "SRS7663855", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.92334, null, 0.08864, null, 0.97611, null, 0.54523, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Canada", "2020-11-06", "Undetermined", "Adult", "Brain", "Nervous System"], [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", null, "pubmed:34054419;pubmed:35204047", null, "injured telencephalic hemisphere 2", "GSM4887528", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:injury", "GSM4887528", "GSM4887528: injured telencephalic hemisphere 2; Danio rerio; RNA Seq", "GSM4887528", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 349593244, 293016325, 377668555, 471810417, 0, "SRX9450940", "SRS7663854", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.93253, null, 0.08588, null, 0.97666, null, 0.54494, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Canada", "2020-11-06", "Undetermined", "Adult", "Brain", "Nervous System"], [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", null, "pubmed:34054419;pubmed:35204047", null, "injured telencephalic hemisphere 1", "GSM4887527", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:injury", "GSM4887527", "GSM4887527: injured telencephalic hemisphere 1; Danio rerio; RNA Seq", "GSM4887527", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 446653242, 378509659, 482923940, 607602368, 0, "SRX9450939", "SRS7663853", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.91949, null, 0.08917, null, 0.97954, null, 0.53009, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Canada", "2020-11-06", "Undetermined", "Adult", "Brain", "Nervous System"], [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", null, "pubmed:34054419;pubmed:35204047", null, "healthy telencephalic hemisphere 3", "GSM4887526", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:no treatment", "GSM4887526", "GSM4887526: healthy telencephalic hemisphere 3; Danio rerio; RNA Seq", "GSM4887526", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 75720892, 64438959, 80940855, 102467938, 0, "SRX9450938", "SRS7663852", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.91791, null, 0.08755, null, 0.98054, null, 0.5616, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Canada", "2020-11-06", "Undetermined", "Adult", "Brain", "Nervous System"], [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", null, "pubmed:34054419;pubmed:35204047", null, "healthy telencephalic hemisphere 2", "GSM4887525", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:no treatment", "GSM4887525", "GSM4887525: healthy telencephalic hemisphere 2; Danio rerio; RNA Seq", "GSM4887525", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 125553872, 106408524, 133237076, 168053930, 0, "SRX9450937", "SRS7663851", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.92261, null, 0.08906, null, 0.97881, null, 0.55986, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Canada", "2020-11-06", "Undetermined", "Adult", "Brain", "Nervous System"], [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", null, "pubmed:34054419;pubmed:35204047", null, "healthy telencephalic hemisphere 1", "GSM4887524", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:no treatment", "GSM4887524", "GSM4887524: healthy telencephalic hemisphere 1; Danio rerio; RNA Seq", "GSM4887524", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 81497309, 69157722, 86472353, 110585893, 0, "SRX9450936", "SRS7663850", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.91979, null, 0.0902, null, 0.96512, null, 0.56094, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Canada", "2020-11-06", "Undetermined", "Adult", "Brain", "Nervous System"], [68382, "SRR17720609", "SRX13883476", "SRS11752245", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Normoxia IP", "GSM5832287", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832287", "GSM5832287: m7G Normoxia IP; Danio rerio; OTHER", "GSM5832287 r1", "GSM5832287", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m7G_Normoxia_IP_R1.fastq.gz m7G_Normoxia_IP_R2.fastq.gz", "fastq fastq", 6634104000.0, 22113680.0, "GSM5832287 r1", "0:150 1:150", "A:1396464650;C:1688319426;G:2250091870;T:1299109891;N:118163", 150, 150, null, null, 1396464650, 1688319426, 2250091870, 1299109891, 118163, "SRX13883476", "SRS11752245", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.9266, 0.92801, 0.07275, 0.06866, 0.89964, 0.90601, 0.65995, 0.75535, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68383, "SRR17720610", "SRX13883475", "SRS11752244", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Normoxia Input", "GSM5832286", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832286", "GSM5832286: m7G Normoxia Input; Danio rerio; OTHER", "GSM5832286 r1", "GSM5832286", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m7G_Normoxia_Input_R1.fastq.gz m7G_Normoxia_Input_R2.fastq.gz", "fastq fastq", 6839977800.0, 22799926.0, "GSM5832286 r1", "0:150 1:150", "A:1986780958;C:1411210049;G:1509902094;T:1932043482;N:41217", 150, 150, null, null, 1986780958, 1411210049, 1509902094, 1932043482, 41217, "SRX13883475", "SRS11752244", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.89709, 0.89888, 0.21747, 0.21725, 0.70021, 0.69936, 0.50469, 0.51865, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68384, "SRR17720611", "SRX13883474", "SRS11752243", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Hypoxia IP", "GSM5832285", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832285", "GSM5832285: m7G Hypoxia IP; Danio rerio; OTHER", "GSM5832285 r1", "GSM5832285", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m7G_Hypoxia_IP_R1.fastq.gz m7G_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 7282575000.0, 24275250.0, "GSM5832285 r1", "0:150 1:150", "A:1512757767;C:1913587260;G:2472336371;T:1383764924;N:128678", 150, 150, null, null, 1512757767, 1913587260, 2472336371, 1383764924, 128678, "SRX13883474", "SRS11752243", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.94526, 0.9467, 0.05248, 0.05071, 0.91946, 0.91981, 0.69303, 0.78448, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68385, "SRR17720612", "SRX13883473", "SRS11752241", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Hypoxia Input", "GSM5832284", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832284", "GSM5832284: m7G Hypoxia Input; Danio rerio; OTHER", "GSM5832284 r1", "GSM5832284", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m7G_Hypoxia_Input_R1.fastq.gz m7G_Hypoxia_Input_R2.fastq.gz", "fastq fastq", 7492311600.0, 24974372.0, "GSM5832284 r1", "0:150 1:150", "A:2208863421;C:1521950436;G:1608371217;T:2153082842;N:43684", 150, 150, null, null, 2208863421, 1521950436, 1608371217, 2153082842, 43684, "SRX13883473", "SRS11752241", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.89264, 0.89479, 0.23239, 0.23163, 0.70496, 0.70311, 0.51741, 0.52135, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68386, "SRR17720613", "SRX13883472", "SRS11752242", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Normoxia IP", "GSM5832283", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832283", "GSM5832283: m6A Normoxia IP; Danio rerio; OTHER", "GSM5832283 r1", "GSM5832283", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, null, "m6A_Normoxia_IP_R1.fastq.gz m6A_Normoxia_IP_R2.fastq.gz", "fastq fastq", 6583667700.0, 21945559.0, "GSM5832283 r1", "0:150 1:150", "A:1750230540;C:1500991424;G:1592129260;T:1740287575;N:28901", 150, 150, null, null, 1750230540, 1500991424, 1592129260, 1740287575, 28901, "SRX13883472", "SRS11752242", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.87682, 0.87986, 0.18203, 0.17239, 0.74671, 0.7472, 0.55638, 0.55861, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68387, "SRR17720614", "SRX13883471", "SRS11752240", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Normoxia Input", "GSM5832282", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832282", "GSM5832282: m6A Normoxia Input; Danio rerio; OTHER", "GSM5832282 r1", "GSM5832282", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m6A_Normoxia_Input_R1.fastq.gz m6A_Normoxia_Input_R2.fastq.gz", "fastq fastq", 6314076000.0, 21046920.0, "GSM5832282 r1", "0:150 1:150", "A:1815907910;C:1329572814;G:1378464668;T:1790102301;N:28307", 150, 150, null, null, 1815907910, 1329572814, 1378464668, 1790102301, 28307, "SRX13883471", "SRS11752240", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.91754, 0.91835, 0.21273, 0.20993, 0.69702, 0.69625, 0.53456, 0.53763, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68388, "SRR17720615", "SRX13883470", "SRS11752239", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Hypoxia IP", "GSM5832281", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832281", "GSM5832281: m6A Hypoxia IP; Danio rerio; OTHER", "GSM5832281 r1", "GSM5832281", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, null, "m6A_Hypoxia_IP_R1.fastq.gz m6A_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 6490349100.0, 21634497.0, "GSM5832281 r1", "0:150 1:150", "A:1714144102;C:1483635762;G:1606044832;T:1686496024;N:28380", 150, 150, null, null, 1714144102, 1483635762, 1606044832, 1686496024, 28380, "SRX13883470", "SRS11752239", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.87598, 0.88161, 0.16783, 0.16105, 0.74588, 0.74568, 0.55361, 0.55307, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68389, "SRR17720616", "SRX13883469", "SRS11752237", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Hypoxia Input", "GSM5832280", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832280", "GSM5832280: m6A Hypoxia Input; Danio rerio; OTHER", "GSM5832280 r1", "GSM5832280", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m6A_Hypoxia_Input_R1.fastq.gz m6A_Hypoxia_Input_R2.fastq.gz", "fastq fastq", 7054483800.0, 23514946.0, "GSM5832280 r1", "0:150 1:150", "A:2000164754;C:1513377207;G:1570441784;T:1970468107;N:31948", 150, 150, null, null, 2000164754, 1513377207, 1570441784, 1970468107, 31948, "SRX13883469", "SRS11752237", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.91916, 0.91997, 0.21403, 0.21158, 0.69716, 0.69503, 0.52616, 0.51982, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68390, "SRR17720617", "SRX13883468", "SRS11752238", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m5C Normoxia IP", "GSM5832279", null, "source name:zebrafish brain tissue|tissue:brain", "m5C Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832279", "GSM5832279: m5C Normoxia IP; Danio rerio; OTHER", "GSM5832279 r1", "GSM5832279", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m5C_Normoxia_IP_R1.fastq.gz m5C_Normoxia_IP_R2.fastq.gz", "fastq fastq", 7385723100.0, 24619077.0, "GSM5832279 r1", "0:150 1:150", "A:1779838658;C:1853060139;G:2010257354;T:1742536078;N:30871", 150, 150, null, null, 1779838658, 1853060139, 2010257354, 1742536078, 30871, "SRX13883468", "SRS11752238", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.88617, 0.87633, 0.42619, 0.41974, 0.71792, 0.74016, 0.69827, 0.68649, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68391, "SRR17720618", "SRX13883467", "SRS11752236", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m5C Normoxia Input", "GSM5832278", null, "source name:zebrafish brain tissue|tissue:brain", "m5C Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832278", "GSM5832278: m5C Normoxia Input; Danio rerio; OTHER", "GSM5832278 r1", "GSM5832278", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m5C_Normoxia_Input_R1.fastq.gz m5C_Normoxia_Input_R2.fastq.gz", "fastq fastq", 6594811500.0, 21982705.0, "GSM5832278 r1", "0:150 1:150", "A:1941068575;C:1341378672;G:1414823713;T:1897501503;N:39037", 150, 150, null, null, 1941068575, 1341378672, 1414823713, 1897501503, 39037, "SRX13883467", "SRS11752236", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.89423, 0.89602, 0.22595, 0.2243, 0.70212, 0.70112, 0.52954, 0.52253, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68392, "SRR17720619", "SRX13883466", "SRS11752235", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m5C Hypoxia IP", "GSM5832277", null, "source name:zebrafish brain tissue|tissue:brain", "m5C Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832277", "GSM5832277: m5C Hypoxia IP; Danio rerio; OTHER", "GSM5832277 r1", "GSM5832277", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m5C_Hypoxia_IP_R1.fastq.gz m5C_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 7837067100.0, 26123557.0, "GSM5832277 r1", "0:150 1:150", "A:1881167242;C:1973697370;G:2143523979;T:1838645554;N:32955", 150, 150, null, null, 1881167242, 1973697370, 2143523979, 1838645554, 32955, "SRX13883466", "SRS11752235", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.87593, 0.87108, 0.45438, 0.45093, 0.71664, 0.7321, 0.67861, 0.69742, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68393, "SRR17720620", "SRX13883465", "SRS11752233", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m5C Hypoxia Input", "GSM5832276", null, "source name:zebrafish brain tissue|tissue:brain", "m5C Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832276", "GSM5832276: m5C Hypoxia Input; Danio rerio; OTHER", "GSM5832276 r1", "GSM5832276", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m5C_Hypoxia_Input_R1.fastq.gz m5C_Hypoxia_Input_R2.fastq.gz", "fastq fastq", 8696183100.0, 28987277.0, "GSM5832276 r1", "0:150 1:150", "A:2564166903;C:1771446935;G:1858965930;T:2501551942;N:51390", 150, 150, null, null, 2564166903, 1771446935, 1858965930, 2501551942, 51390, "SRX13883465", "SRS11752233", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.89379, 0.89585, 0.23898, 0.23828, 0.70272, 0.70278, 0.52965, 0.50047, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68394, "SRR17720621", "SRX13883464", "SRS11752234", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m1A Normoxia IP", "GSM5832275", null, "source name:zebrafish brain tissue|tissue:brain", "m1A Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832275", "GSM5832275: m1A Normoxia IP; Danio rerio; OTHER", "GSM5832275 r1", "GSM5832275", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m1A_Normoxia_IP_R1.fastq.gz m1A_Normoxia_IP_R2.fastq.gz", "fastq fastq", 6882734400.0, 22942448.0, "GSM5832275 r1", "0:150 1:150", "A:1321946139;C:1977632664;G:2310916241;T:1272200359;N:38997", 150, 150, null, null, 1321946139, 1977632664, 2310916241, 1272200359, 38997, "SRX13883464", "SRS11752234", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.88367, 0.88951, 0.09774, 0.09525, 0.86395, 0.86401, 0.70125, 0.74894, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68395, "SRR17720622", "SRX13883463", "SRS11752232", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m1A Normoxia Input", "GSM5832274", null, "source name:zebrafish brain tissue|tissue:brain", "m1A Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832274", "GSM5832274: m1A Normoxia Input; Danio rerio; OTHER", "GSM5832274 r1", "GSM5832274", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m1A_Normoxia_Input_R1.fastq.gz m1A_Normoxia_Input_R2.fastq.gz", "fastq fastq", 7374452700.0, 24581509.0, "GSM5832274 r1", "0:150 1:150", "A:1511389847;C:2082118937;G:2325922232;T:1454979400;N:42284", 150, 150, null, null, 1511389847, 2082118937, 2325922232, 1454979400, 42284, "SRX13883463", "SRS11752232", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.94589, 0.94385, 0.18226, 0.18222, 0.80878, 0.8102, 0.73686, 0.71921, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68396, "SRR17720623", "SRX13883462", "SRS11752231", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m1A Hypoxia IP", "GSM5832273", null, "source name:zebrafish brain tissue|tissue:brain", "m1A Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832273", "GSM5832273: m1A Hypoxia IP; Danio rerio; OTHER", "GSM5832273 r1", "GSM5832273", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m1A_Hypoxia_IP_R1.fastq.gz m1A_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 4861573800.0, 16205246.0, "GSM5832273 r1", "0:150 1:150", "A:927063480;C:1355342107;G:1698345464;T:880801957;N:20792", 150, 150, null, null, 927063480, 1355342107, 1698345464, 880801957, 20792, "SRX13883462", "SRS11752231", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.8575, 0.86165, 0.10013, 0.09909, 0.87249, 0.87221, 0.72225, 0.66629, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68397, "SRR17720624", "SRX13883461", "SRS11752229", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m1A Hypoxia Input", "GSM5832272", null, "source name:zebrafish brain tissue|tissue:brain", "m1A Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832272", "GSM5832272: m1A Hypoxia Input; Danio rerio; OTHER", "GSM5832272 r1", "GSM5832272", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m1A_Hypoxia_Input_R1.fastq.gz m1A_Hypoxia_Input_R2.fastq.gz", "fastq fastq", 7262130600.0, 24207102.0, "GSM5832272 r1", "0:150 1:150", "A:1553326396;C:2003023914;G:2214285414;T:1491453374;N:41502", 150, 150, null, null, 1553326396, 2003023914, 2214285414, 1491453374, 41502, "SRX13883461", "SRS11752229", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.94247, 0.94013, 0.20625, 0.20507, 0.80188, 0.80137, 0.70188, 0.73891, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68398, "SRR17720625", "SRX13883460", "SRS11752230", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "mRNA Normoxia", "GSM5832271", null, "source name:zebrafish brain tissue|tissue:brain", "mRNA Normoxia", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832271", "GSM5832271: mRNA Normoxia; Danio rerio; RNA Seq", "GSM5832271 r1", "GSM5832271", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "mRNA_Normoxia_R1.fastq.gz mRNA_Normoxia_R2.fastq.gz", "fastq fastq", 5600123100.0, 18667077.0, "GSM5832271 r1", "0:150 1:150", "A:1581506491;C:1211015791;G:1232941851;T:1574629930;N:29037", 150, 150, null, null, 1581506491, 1211015791, 1232941851, 1574629930, 29037, "SRX13883460", "SRS11752230", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.88183, 0.88417, 0.48505, 0.47939, 0.71914, 0.71867, 0.49613, 0.50205, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68399, "SRR17720626", "SRX13883459", "SRS11752228", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "mRNA Hypoxia", "GSM5832270", null, "source name:zebrafish brain tissue|tissue:brain", "mRNA Hypoxia", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832270", "GSM5832270: mRNA Hypoxia; Danio rerio; RNA Seq", "GSM5832270 r1", "GSM5832270", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "mRNA_Hypoxia_R1.fastq.gz mRNA_Hypoxia_R2.fastq.gz", "fastq fastq", 5576898600.0, 18589662.0, "GSM5832270 r1", "0:150 1:150", "A:1567886841;C:1214001571;G:1233723295;T:1561258221;N:28672", 150, 150, null, null, 1567886841, 1214001571, 1233723295, 1561258221, 28672, "SRX13883459", "SRS11752228", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.88472, 0.88798, 0.46504, 0.45892, 0.72005, 0.71752, 0.49715, 0.51843, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [70159, "SRR19560554", "SRX15612628", "SRS13313406", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a WT4", "GSM6215039", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT", "dyrk1a WT4", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT", "GSM6215039", "GSM6215039: dyrk1a WT4; Danio rerio; RNA Seq", "GSM6215039 r1", "GSM6215039", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_WT4_055_138_S10_L001_R1_001.fastq.gz dyrk1a_WT4_055_138_S10_L001_R2_001.fastq.gz", "fastq fastq", 7902803378.0, 39122789.0, "GSM6215039 r1", "0:101 1:101", "A:2306156032;C:1634172814;G:1752044587;T:2210254720;N:175225", 101, 101, null, null, 2306156032, 1634172814, 1752044587, 2210254720, 175225, "SRX15612628", "SRS13313406", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.89674, 0.89785, 0.11283, 0.1133, 0.69455, 0.69355, 0.4786, 0.47508, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70160, "SRR19560555", "SRX15612627", "SRS13313405", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a WT2", "GSM6215038", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT", "dyrk1a WT2", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT", "GSM6215038", "GSM6215038: dyrk1a WT2; Danio rerio; RNA Seq", "GSM6215038 r1", "GSM6215038", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_WT2_067_126_S9_L001_R1_001.fastq.gz dyrk1a_WT2_067_126_S9_L001_R2_001.fastq.gz", "fastq fastq", 7079496222.0, 35047011.0, "GSM6215038 r1", "0:101 1:101", "A:2065386157;C:1460884924;G:1579377775;T:1973689055;N:158311", 101, 101, null, null, 2065386157, 1460884924, 1579377775, 1973689055, 158311, "SRX15612627", "SRS13313405", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.89733, 0.89769, 0.10808, 0.1082, 0.69473, 0.69246, 0.4714, 0.46904, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70161, "SRR19560556", "SRX15612626", "SRS13313404", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a WT1", "GSM6215037", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT", "dyrk1a WT1", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:dyrk1a WT", "GSM6215037", "GSM6215037: dyrk1a WT1; Danio rerio; RNA Seq", "GSM6215037 r1", "GSM6215037", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_WT1_079_114_S8_L001_R1_001.fastq.gz dyrk1a_WT1_079_114_S8_L001_R2_001.fastq.gz", "fastq fastq", 6622132670.0, 32782835.0, "GSM6215037 r1", "0:101 1:101", "A:1948249689;C:1344786648;G:1444984183;T:1883963959;N:148191", 101, 101, null, null, 1948249689, 1344786648, 1444984183, 1883963959, 148191, "SRX15612626", "SRS13313404", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.88644, 0.8854, 0.1325, 0.13284, 0.69745, 0.69455, 0.48645, 0.48809, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70162, "SRR19560557", "SRX15612625", "SRS13313403", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a HET4", "GSM6215036", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET", "dyrk1a HET4", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET", "GSM6215036", "GSM6215036: dyrk1a HET4; Danio rerio; RNA Seq", "GSM6215036 r1", "GSM6215036", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_Het4_091_102_S7_L001_R1_001.fastq.gz dyrk1a_Het4_091_102_S7_L001_R2_001.fastq.gz", "fastq fastq", 6825687060.0, 33790530.0, "GSM6215036 r1", "0:101 1:101", "A:1996927388;C:1382413394;G:1491219728;T:1954975088;N:151462", 101, 101, null, null, 1996927388, 1382413394, 1491219728, 1954975088, 151462, "SRX15612625", "SRS13313403", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.8771, 0.87636, 0.13953, 0.13921, 0.70134, 0.70082, 0.48309, 0.49155, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70163, "SRR19560558", "SRX15612624", "SRS13313402", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a HET3", "GSM6215035", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET", "dyrk1a HET3", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET", "GSM6215035", "GSM6215035: dyrk1a HET3; Danio rerio; RNA Seq", "GSM6215035 r1", "GSM6215035", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_Het3_008_185_S6_L001_R1_001.fastq.gz dyrk1a_Het3_008_185_S6_L001_R2_001.fastq.gz", "fastq fastq", 9512968204.0, 47093902.0, "GSM6215035 r1", "0:101 1:101", "A:2793571739;C:1936475456;G:2088476685;T:2694233049;N:211275", 101, 101, null, null, 2793571739, 1936475456, 2088476685, 2694233049, 211275, "SRX15612624", "SRS13313402", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.88305, 0.88109, 0.13901, 0.13926, 0.69856, 0.69615, 0.48988, 0.48919, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70164, "SRR19560559", "SRX15612623", "SRS13313401", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a HET2", "GSM6215034", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET", "dyrk1a HET2", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:dyrk1a HET", "GSM6215034", "GSM6215034: dyrk1a HET2; Danio rerio; RNA Seq", "GSM6215034 r1", "GSM6215034", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_Het2_020_173_S5_L001_R1_001.fastq.gz dyrk1a_Het2_020_173_S5_L001_R2_001.fastq.gz", "fastq fastq", 7644875638.0, 37845919.0, "GSM6215034 r1", "0:101 1:101", "A:2190708434;C:1609961798;G:1719044598;T:2124991128;N:169680", 101, 101, null, null, 2190708434, 1609961798, 1719044598, 2124991128, 169680, "SRX15612623", "SRS13313401", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.893, 0.89318, 0.07847, 0.07861, 0.69325, 0.69191, 0.4503, 0.45105, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70165, "SRR19560560", "SRX15612622", "SRS13313400", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a HOM5", "GSM6215033", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "dyrk1a HOM5", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "GSM6215033", "GSM6215033: dyrk1a HOM5; Danio rerio; RNA Seq", "GSM6215033 r1", "GSM6215033", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_Hom5_032_161_S4_L001_R1_001.fastq.gz dyrk1a_Hom5_032_161_S4_L001_R2_001.fastq.gz", "fastq fastq", 6286655716.0, 31122058.0, "GSM6215033 r1", "0:101 1:101", "A:1884291009;C:1241960690;G:1345362712;T:1814899144;N:142161", 101, 101, null, null, 1884291009, 1241960690, 1345362712, 1814899144, 142161, "SRX15612622", "SRS13313400", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.8708, 0.87099, 0.1837, 0.18358, 0.71346, 0.71043, 0.52327, 0.52172, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70166, "SRR19560561", "SRX15612621", "SRS13313399", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a HOM3", "GSM6215032", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "dyrk1a HOM3", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "GSM6215032", "GSM6215032: dyrk1a HOM3; Danio rerio; RNA Seq", "GSM6215032 r1", "GSM6215032", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_Hom3_044_149_S3_L001_R1_001.fastq.gz dyrk1a_Hom3_044_149_S3_L001_R2_001.fastq.gz", "fastq fastq", 7148763840.0, 35389920.0, "GSM6215032 r1", "0:101 1:101", "A:2092747707;C:1464796550;G:1572724974;T:2018333200;N:161409", 101, 101, null, null, 2092747707, 1464796550, 1572724974, 2018333200, 161409, "SRX15612621", "SRS13313399", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.88908, 0.88682, 0.13424, 0.13371, 0.69203, 0.6913, 0.49374, 0.49311, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70167, "SRR19560562", "SRX15612620", "SRS13313398", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a HOM2", "GSM6215031", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "dyrk1a HOM2", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "GSM6215031", "GSM6215031: dyrk1a HOM2; Danio rerio; RNA Seq", "GSM6215031 r1", "GSM6215031", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_Hom2_056_137_S2_L001_R1_001.fastq.gz dyrk1a_Hom2_056_137_S2_L001_R2_001.fastq.gz", "fastq fastq", 5786861054.0, 28647827.0, "GSM6215031 r1", "0:101 1:101", "A:1671012970;C:1197032060;G:1296060748;T:1622623090;N:132186", 101, 101, null, null, 1671012970, 1197032060, 1296060748, 1622623090, 132186, "SRX15612620", "SRS13313398", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.88887, 0.88943, 0.08816, 0.08816, 0.69262, 0.68994, 0.47509, 0.47239, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70168, "SRR19560563", "SRX15612619", "SRS13313397", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "dyrk1a HOM1", "GSM6215030", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "dyrk1a HOM1", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:dyrk1a HOM", "GSM6215030", "GSM6215030: dyrk1a HOM1; Danio rerio; RNA Seq", "GSM6215030 r1", "GSM6215030", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "dyrk1a_Hom1_068_125_S1_L001_R1_001.fastq.gz dyrk1a_Hom1_068_125_S1_L001_R2_001.fastq.gz", "fastq fastq", 6721969150.0, 33277075.0, "GSM6215030 r1", "0:101 1:101", "A:1943487755;C:1388497581;G:1509724133;T:1880112182;N:147499", 101, 101, null, null, 1943487755, 1388497581, 1509724133, 1880112182, 147499, "SRX15612619", "SRS13313397", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.892, 0.89258, 0.08973, 0.09, 0.69804, 0.69619, 0.47477, 0.47297, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70169, "SRR19560573", "SRX15612609", "SRS13313387", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab WT3", "GSM6215020", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT", "scn1lab WT3", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT", "GSM6215020", "GSM6215020: scn1lab WT3; Danio rerio; RNA Seq", "GSM6215020 r1", "GSM6215020", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_WT3_R1.fastq.gz Dec8_scn1_WT3_R2.fastq.gz", "fastq fastq", 8755553246.0, 43344323.0, "GSM6215020 r1", "0:101 1:101", "A:2522756407;C:1825383888;G:2009734783;T:2397482724;N:195444", 101, 101, null, null, 2522756407, 1825383888, 2009734783, 2397482724, 195444, "SRX15612609", "SRS13313387", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.88631, 0.89209, 0.13849, 0.13882, 0.68359, 0.68373, 0.48499, 0.48536, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70170, "SRR19560574", "SRX15612608", "SRS13313386", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab WT2", "GSM6215019", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT", "scn1lab WT2", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT", "GSM6215019", "GSM6215019: scn1lab WT2; Danio rerio; RNA Seq", "GSM6215019 r1", "GSM6215019", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_WT2_R1.fastq.gz Dec8_scn1_WT2_R2.fastq.gz", "fastq fastq", 9208034256.0, 45584328.0, "GSM6215019 r1", "0:101 1:101", "A:2708559207;C:1845326645;G:2043146078;T:2610799023;N:203303", 101, 101, null, null, 2708559207, 1845326645, 2043146078, 2610799023, 203303, "SRX15612608", "SRS13313386", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.8783, 0.88175, 0.15498, 0.15526, 0.69031, 0.68935, 0.5029, 0.50682, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70171, "SRR19560575", "SRX15612607", "SRS13313385", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab WT1", "GSM6215018", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT", "scn1lab WT1", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Wild type|genotype:scn1lab WT", "GSM6215018", "GSM6215018: scn1lab WT1; Danio rerio; RNA Seq", "GSM6215018 r1", "GSM6215018", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_WT1_R1.fastq.gz Dec8_scn1_WT1_R2.fastq.gz", "fastq fastq", 8866777880.0, 43894940.0, "GSM6215018 r1", "0:101 1:101", "A:2619286212;C:1773731842;G:1954443989;T:2519120249;N:195588", 101, 101, null, null, 2619286212, 1773731842, 1954443989, 2519120249, 195588, "SRX15612607", "SRS13313385", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.87792, 0.87896, 0.1645, 0.16446, 0.69873, 0.69767, 0.50758, 0.50857, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70172, "SRR19560576", "SRX15612606", "SRS13313384", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab HET3", "GSM6215017", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET", "scn1lab HET3", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET", "GSM6215017", "GSM6215017: scn1lab HET3; Danio rerio; RNA Seq", "GSM6215017 r1", "GSM6215017", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_HET3_R1.fastq.gz Dec8_scn1_HET3_R2.fastq.gz", "fastq fastq", 9837485850.0, 48700425.0, "GSM6215017 r1", "0:101 1:101", "A:3058002601;C:1783589847;G:1999426374;T:2996247689;N:219339", 101, 101, null, null, 3058002601, 1783589847, 1999426374, 2996247689, 219339, "SRX15612606", "SRS13313384", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.79228, 0.79265, 0.19829, 0.19897, 0.768, 0.76881, 0.63874, 0.60993, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70173, "SRR19560577", "SRX15612605", "SRS13313383", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab HET2", "GSM6215016", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET", "scn1lab HET2", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET", "GSM6215016", "GSM6215016: scn1lab HET2; Danio rerio; RNA Seq", "GSM6215016 r1", "GSM6215016", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_HET2_R1.fastq.gz Dec8_scn1_HET2_R2.fastq.gz", "fastq fastq", 7904076382.0, 39129091.0, "GSM6215016 r1", "0:101 1:101", "A:2313856206;C:1597073570;G:1729185251;T:2263789669;N:171686", 101, 101, null, null, 2313856206, 1597073570, 1729185251, 2263789669, 171686, "SRX15612605", "SRS13313383", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.87286, 0.87498, 0.13182, 0.13228, 0.72001, 0.71989, 0.54792, 0.5451, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70174, "SRR19560578", "SRX15612604", "SRS13313381", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab HET1", "GSM6215015", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET", "scn1lab HET1", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Heterozygous|genotype:scn1lab HET", "GSM6215015", "GSM6215015: scn1lab HET1; Danio rerio; RNA Seq", "GSM6215015 r1", "GSM6215015", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_HET1_R1.fastq.gz Dec8_scn1_HET1_R2.fastq.gz", "fastq fastq", 10583641934.0, 52394267.0, "GSM6215015 r1", "0:101 1:101", "A:3069468722;C:2179597536;G:2345048883;T:2989294494;N:232299", 101, 101, null, null, 3069468722, 2179597536, 2345048883, 2989294494, 232299, "SRX15612604", "SRS13313381", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.87752, 0.8777, 0.12364, 0.12313, 0.71654, 0.71737, 0.48643, 0.47848, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70175, "SRR19560579", "SRX15612603", "SRS13313382", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab HOM3", "GSM6215014", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM", "scn1lab HOM3", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM", "GSM6215014", "GSM6215014: scn1lab HOM3; Danio rerio; RNA Seq", "GSM6215014 r1", "GSM6215014", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_HOM3_R1.fastq.gz Dec8_scn1_HOM3_R2.fastq.gz", "fastq fastq", 7777420766.0, 38502083.0, "GSM6215014 r1", "0:101 1:101", "A:2213965945;C:1621764946;G:1767224135;T:2174292493;N:173247", 101, 101, null, null, 2213965945, 1621764946, 1767224135, 2174292493, 173247, "SRX15612603", "SRS13313382", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.88412, 0.88408, 0.09074, 0.09152, 0.72338, 0.72403, 0.51741, 0.51684, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70176, "SRR19560580", "SRX15612602", "SRS13313380", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab HOM2", "GSM6215013", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM", "scn1lab HOM2", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM", "GSM6215013", "GSM6215013: scn1lab HOM2; Danio rerio; RNA Seq", "GSM6215013 r1", "GSM6215013", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_HOM2_R1.fastq.gz Dec8_scn1_HOM2_R2.fastq.gz", "fastq fastq", 8568922820.0, 42420410.0, "GSM6215013 r1", "0:101 1:101", "A:2555761269;C:1697178868;G:1896122512;T:2419672664;N:187507", 101, 101, null, null, 2555761269, 1697178868, 1896122512, 2419672664, 187507, "SRX15612602", "SRS13313380", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.87147, 0.87346, 0.14976, 0.14929, 0.70571, 0.70611, 0.52591, 0.52781, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70177, "SRR19560581", "SRX15612601", "SRS13313379", "SRP378803", "PRJNA846486", "High throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways", "GSE205578", "Transcriptome Analysis", "Investigation of convergence and divergence of different Autism Risk genes at the molecular level  in the brain of zebrafish ASD mutants at 6 dpf dpf Overall design: Comparative gene expression profiling analysis of bulk RNA seq data of the high confidence Autism Risk Genes: scn1lab and dyrk1a.", null, "pubmed:36933215", null, "scn1lab HOM1", "GSM6215012", null, "source name:Whole Brain|tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM", "scn1lab HOM1", "DESeq2 v 1.22.1 Low quality reads were trimmed and adaptor contamination was removed using Trim Galore v0.5.0  https://www.bioinformatics.babraham.ac.uk/projects/trim galore/ Trimmed reads were mapped to the Danio rerio reference genome GRCz11 using HISAT2 v2.1.0 Kim et al.  2019 Gene expression levels were quantified using StringTie v1.3.3b Pertea et al.  2015 with gene models release 103 from the Ensembl Differentially expressed genes adjusted p value < 0.05  fold change cutoff = 2 were identified using DESeq2 v 1.22.1 Love et al.  2014 Assembly: GRCz11 Supplementary files format and content: tab delimited CSV files include read values for each Sample", "Whole Brain", null, "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "tissue:Whole Brain|cell type:whole brain cells|genotype:Homozygous|genotype:scn1lab HOM", "GSM6215012", "GSM6215012: scn1lab HOM1; Danio rerio; RNA Seq", "GSM6215012 r1", "GSM6215012", "1", "Total RNA was extracted from isolated larval heads with the eyes removed 1 head per sample using the RNeasy Micro Kit Qiagen or the Invitrogen RecoverAll  RNA Isolation Kit Invitrogen. To control for background variation  RNA was extracted from sibling  or cousin matched larvae from heterozygous incrosses of scn1lab\u039444/+  chd8\u03945/+ and dyrk1aa\u039477/+:dyrk1ab\u03948/+ fish RNA library preparation was performed using NEBNext Single Cell Low Input RNA Library Prep Kit Cat# E6420L Sequencing was done at 25 million reads/sample using NovaSeq 6000 Illumina Yale Center for Genome Analysis", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP378803", null, "loader:fastq load.py", "Dec8_scn1_HOM1_R1.fastq.gz Dec8_scn1_HOM1_R2.fastq.gz", "fastq fastq", 7104138808.0, 35169004.0, "GSM6215012 r1", "0:101 1:101", "A:2086867330;C:1422921410;G:1555208321;T:2038985303;N:156444", 101, 101, null, null, 2086867330, 1422921410, 1555208321, 2038985303, 156444, "SRX15612601", "SRS13313379", "SRA1432967", "Hoffman Lab, Neuroscience, Yale University", "Hoffman Lab, Neuroscience, Yale University", 2, 0.86112, 0.86909, 0.13235, 0.13356, 0.72143, 0.72092, 0.42339, 0.43557, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-06-06", "Larval", "Larval", "Brain", "Nervous System"], [70436, "SRR19846950", "SRX15890625", "SRS13579729", "SRP383494", "PRJNA852585", "Control of cranial ectomesenchyme fate by Nr2f nuclear receptors", "GSE206903", "Transcriptome Analysis", "Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches  they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition  the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a  prrx1a/b  sox9a  twist1a  and fli1a  and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype  mutants partially or fully recover  likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants  while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.", null, "pubmed:36367707", null, "sox10:DsRed+ neural crest cells from 20 hpf wild type embryos   biol rep 2", "GSM6266712", null, "tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf", "sox10:DsRed+ neural crest cells from 20 hpf wild type embryos   biol rep 2", "Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript.", "sox10:DsRed+ neural crest cells", null, "Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input  and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters  assessed by Bioanalyzer  and quantified using the Kapa Library Quantification kit.", null, "cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf", "GSM6266712", "GSM6266712: sox10:DsRed+ neural crest cells from 20 hpf wild type embryos   biol rep 2; Danio rerio; RNA Seq", "GSM6266712 r1", "GSM6266712", "1", "Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input  and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters  assessed by Bioanalyzer  and quantified using the Kapa Library Quantification kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP383494", null, "loader:fastq load.py", "sox10DsRed-CON2-S6-R1.fastq.gz sox10DsRed-CON2-S6_R2_001.fastq.gz", "fastq fastq", 4876722704.0, 32083702.0, "GSM6266712 r1", "0:76 1:76", "A:1342673931;C:1107276249;G:1150211941;T:1276364234;N:196349", 76, 76, null, null, 1342673931, 1107276249, 1150211941, 1276364234, 196349, "SRX15890625", "SRS13579729", null, null, "Human Genetics, Cincinnati Children's Hospital Medical Center", 2, 0.8977, 0.90038, 0.03951, 0.04044, 0.75777, 0.76331, 0.46312, 0.4722, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "United States", "2022-06-24", "Segmentation", "Embryo", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 148, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "bulk", "p2": "Brain"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Brain", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 132, "toggle_url": 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