rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
10391,ERR8516975,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R,0:51 1:51,A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852,51,51,,,1077092958,949537387,955020348,1099432979,20556852,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.9053,0.9259,0.21658,0.22155,0.69369,0.69179,0.50726,0.50871,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10392,ERR8516976,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R,0:51 1:51,A:972081222;C:890179393;G:888655698;T:998443264;N:18934747,51,51,,,972081222,890179393,888655698,998443264,18934747,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.86107,0.87807,0.22063,0.23029,0.70859,0.70561,0.51656,0.51946,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10393,ERR8516977,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R,0:51 1:51,A:728798881;C:962223604;G:958876331;T:735449513;N:17094231,51,51,,,728798881,962223604,958876331,735449513,17094231,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.54616,0.55881,0.13313,0.14036,0.84295,0.84185,0.64193,0.59762,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10394,ERR8516972,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R,0:51 1:51,A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786,51,51,,,837274632,1062368015,1049892288,853310517,19213786,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.5726,0.57788,0.13781,0.14082,0.80616,0.80452,0.61581,0.60389,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10395,ERR8516973,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R,0:51 1:51,A:897813231;C:796012893;G:794839496;T:923696030;N:17221274,51,51,,,897813231,796012893,794839496,923696030,17221274,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.92095,0.94156,0.18892,0.20024,0.6901,0.68905,0.49377,0.50086,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10396,ERR8516974,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R,0:51 1:51,A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248,51,51,,,951912827,1107150666,1086060798,973791571,20785248,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.63792,0.62667,0.18547,0.18671,0.78756,0.78549,0.59274,0.55478,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10397,ERR8516969,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R,0:51 1:51,A:925784769;C:934445856;G:959155668;T:924080408;N:18878983,51,51,,,925784769,934445856,959155668,924080408,18878983,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.59503,0.61112,0.1947,0.20225,0.76512,0.76337,0.54584,0.54345,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10398,ERR8516970,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R,0:51 1:51,A:991755033;C:864808531;G:892202564;T:992188806;N:18881958,51,51,,,991755033,864808531,892202564,992188806,18881958,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.86612,0.88689,0.26181,0.2728,0.7094,0.7091,0.53639,0.53906,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10399,ERR8516971,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R,0:51 1:51,A:766707527;C:798667604;G:818782599;T:773280942;N:15938306,51,51,,,766707527,798667604,818782599,773280942,15938306,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.88811,0.92834,0.21869,0.22669,0.72878,0.72604,0.55598,0.57831,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10400,ERR8516966,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R,0:51 1:51,A:774360373;C:720215184;G:719479745;T:796239200;N:15182374,51,51,,,774360373,720215184,719479745,796239200,15182374,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.79643,0.81194,0.25554,0.2603,0.72236,0.72021,0.51775,0.51678,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10401,ERR8516967,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R,0:51 1:51,A:739921027;C:667375549;G:663864111;T:764302396;N:14288091,51,51,,,739921027,667375549,663864111,764302396,14288091,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.90817,0.92909,0.23387,0.24814,0.70088,0.69842,0.51238,0.51267,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10402,ERR8516968,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X9_190227_A00421_38_AH7523DRXX_S49_R1_001.fastq.gz 15812X9_190227_A00421_38_AH7523DRXX_S49_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X9 190227 A00421 38 AH7523DRXX S49 R,0:51 1:51,A:882831441;C:935213418;G:957033335;T:879085993;N:18444957,51,51,,,882831441,935213418,957033335,879085993,18444957,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.76218,0.7682,0.18357,0.18521,0.74444,0.74272,0.46714,0.55518,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
11815,ERR11799086,ERX11197445,ERS16222830,ERP149963,PRJEB64798,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E-MTAB-13228,Transcriptome Analysis,We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,Sample 4,SAMEA114237385,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237385|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 4|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 4|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E MTAB 13228:Sample 4 p,Sample 4 p,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP149963,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R1.fq.gz so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R2.fq.gz,fastq fastq,19305011730.0,95569365.0,E MTAB 13228:so zf94 VW4 MDMG7 CD45lo mhc2dab MGA S58 R,0:101 1:101,A:6768262250;C:3044091042;G:2847188942;T:6645295452;N:174044,101,101,,,6768262250,3044091042,2847188942,6645295452,174044,ERX11197445,ERS16222830,ERA26360556,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.57007,0.5231,0.45597,0.40582,0.91579,0.91674,0.58257,0.5625,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,unknown,bulk,bulk,bulk,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
11816,ERR11799088,ERX11197447,ERS16222832,ERP149963,PRJEB64798,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E-MTAB-13228,Transcriptome Analysis,We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,Sample 6,SAMEA114237387,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237387|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 6|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 6|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E MTAB 13228:Sample 6 p,Sample 6 p,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP149963,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R2.fq.gz so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R1.fq.gz,fastq fastq,21028230098.0,104100149.0,E MTAB 13228:so zf94 VW6 MDMF8 CD45hi mhc2dab MACA S60 R,0:101 1:101,A:6738894716;C:4007335499;G:3664578692;T:6617229148;N:192043,101,101,,,6738894716,4007335499,3664578692,6617229148,192043,ERX11197447,ERS16222832,ERA26360556,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.69217,0.69414,0.45934,0.4539,0.86423,0.86344,0.64485,0.62976,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,unknown,bulk,bulk,bulk,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
11817,ERR11799085,ERX11197444,ERS16222829,ERP149963,PRJEB64798,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E-MTAB-13228,Transcriptome Analysis,We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,Sample 3,SAMEA114237384,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237384|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 3|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 3|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E MTAB 13228:Sample 3 p,Sample 3 p,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP149963,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R1.fq.gz so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R2.fq.gz,fastq fastq,20720724286.0,102577843.0,E MTAB 13228:so zf94 VW3 MDMG1 CD45lo mhc2dab MGA S57 R,0:101 1:101,A:7221245295;C:3305546836;G:3154595537;T:7039147315;N:189303,101,101,,,7221245295,3305546836,3154595537,7039147315,189303,ERX11197444,ERS16222829,ERA26360556,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.6027,0.56103,0.46397,0.41738,0.90536,0.90473,0.59858,0.59246,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,unknown,bulk,bulk,bulk,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
11818,ERR11799087,ERX11197446,ERS16222831,ERP149963,PRJEB64798,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E-MTAB-13228,Transcriptome Analysis,We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,Sample 5,SAMEA114237386,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237386|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 5|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 5|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E MTAB 13228:Sample 5 p,Sample 5 p,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP149963,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R2.fq.gz so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R1.fq.gz,fastq fastq,20557799368.0,101771284.0,E MTAB 13228:so zf94 VW5 MDMF2 CD45hi mhc2dab MACA S59 R,0:101 1:101,A:5872430236;C:4635392917;G:4244261404;T:5805533335;N:181476,101,101,,,5872430236,4635392917,4244261404,5805533335,181476,ERX11197446,ERS16222831,ERA26360556,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.48524,0.49426,0.30765,0.31318,0.87008,0.86918,0.60597,0.58678,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,unknown,bulk,bulk,bulk,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
11819,ERR11799083,ERX11197442,ERS16222827,ERP149963,PRJEB64798,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E-MTAB-13228,Transcriptome Analysis,We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,Sample 1,SAMEA114237382,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237382|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 1|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E MTAB 13228:Sample 1 p,Sample 1 p,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP149963,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R2.fq.gz so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R1.fq.gz,fastq fastq,24592452226.0,121744813.0,E MTAB 13228:so zf94 VW1 P2Y12 CD45lo MGA S55 R,0:101 1:101,A:6964719283;C:5587681189;G:5075783189;T:6964040906;N:227659,101,101,,,6964719283,5587681189,5075783189,6964040906,227659,ERX11197442,ERS16222827,ERA26360556,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.82038,0.82668,0.39096,0.39605,0.82532,0.82446,0.63514,0.57014,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,unknown,bulk,bulk,bulk,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
11820,ERR11799084,ERX11197443,ERS16222828,ERP149963,PRJEB64798,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E-MTAB-13228,Transcriptome Analysis,We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,Sample 2,SAMEA114237383,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237383|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 2|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 2|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,E MTAB 13228:Sample 2 p,Sample 2 p,Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set,,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP149963,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R2.fq.gz so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R1.fq.gz,fastq fastq,23692841994.0,117291297.0,E MTAB 13228:so zf94 VW2 P2Y12 CD45lo MGA S56 R,0:101 1:101,A:6997658831;C:5103576511;G:4615471075;T:6975924499;N:211078,101,101,,,6997658831,5103576511,4615471075,6975924499,211078,ERX11197443,ERS16222828,ERA26360556,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.78961,0.79279,0.39456,0.39476,0.8227,0.82309,0.62072,0.61776,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,unknown,bulk,bulk,bulk,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
26484,SRR26034368,SRX21751589,SRS18859096,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X9 tp53mut control,GSM7774465,,source name:brain|tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X9 tp53mut control,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant,GSM7774465,GSM7774465: 19521X9 tp53mut control; Danio rerio; RNA Seq,GSM7774465 r1,GSM7774465,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X9_220211_A00421_0418_AHGVTMDSX3_S180_L003_R2_001.fastq.gz 19521X9_220211_A00421_0418_AHGVTMDSX3_S180_L003_R1_001.fastq.gz,fastq fastq,13111362918.0,43415109.0,GSM7774465 r1,0:151 1:151,A:3716297698;C:2842682328;G:2964203082;T:3588045151;N:134659,151,151,,,3716297698,2842682328,2964203082,3588045151,134659,SRX21751589,SRS18859096,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.87652,0.87774,0.39216,0.39133,0.71102,0.71133,0.53264,0.53118,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Adult,Adult,Brain,Nervous System
26485,SRR26034369,SRX21751588,SRS18859094,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X8 tp53mut control,GSM7774464,,source name:brain|tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X8 tp53mut control,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant,GSM7774464,GSM7774464: 19521X8 tp53mut control; Danio rerio; RNA Seq,GSM7774464 r1,GSM7774464,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X8_220211_A00421_0418_AHGVTMDSX3_S179_L003_R1_001.fastq.gz 19521X8_220211_A00421_0418_AHGVTMDSX3_S179_L003_R2_001.fastq.gz,fastq fastq,13892147074.0,46000487.0,GSM7774464 r1,0:151 1:151,A:3814725425;C:3130415629;G:3297762528;T:3649099178;N:144314,151,151,,,3814725425,3130415629,3297762528,3649099178,144314,SRX21751588,SRS18859094,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89624,0.89685,0.34529,0.34496,0.70092,0.70335,0.53129,0.53612,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Adult,Adult,Brain,Nervous System
26486,SRR26034370,SRX21751587,SRS18859095,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X7 tp53mut control,GSM7774463,,source name:brain|tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X7 tp53mut control,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:control|age:1 year|genotype:tp53 mutant,GSM7774463,GSM7774463: 19521X7 tp53mut control; Danio rerio; RNA Seq,GSM7774463 r1,GSM7774463,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X7_220211_A00421_0418_AHGVTMDSX3_S178_L003_R1_001.fastq.gz 19521X7_220211_A00421_0418_AHGVTMDSX3_S178_L003_R2_001.fastq.gz,fastq fastq,15619675560.0,51720780.0,GSM7774463 r1,0:151 1:151,A:4385995044;C:3423475528;G:3608910971;T:4201133585;N:160432,151,151,,,4385995044,3423475528,3608910971,4201133585,160432,SRX21751587,SRS18859095,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.88198,0.88184,0.36824,0.36836,0.70138,0.70427,0.50325,0.50812,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Adult,Adult,Brain,Nervous System
26487,SRR26034371,SRX21751586,SRS18859093,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X6 tp53het tumor,GSM7774462,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X6 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774462,GSM7774462: 19521X6 tp53het tumor; Danio rerio; RNA Seq,GSM7774462 r1,GSM7774462,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R1_001.fastq.gz 19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R2_001.fastq.gz,fastq fastq,13856710696.0,45883148.0,GSM7774462 r1,0:151 1:151,A:3910050404;C:3019565763;G:3183961340;T:3742992264;N:140925,151,151,,,3910050404,3019565763,3183961340,3742992264,140925,SRX21751586,SRS18859093,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.8794,0.87909,0.38495,0.38479,0.69753,0.70005,0.49322,0.49442,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26488,SRR26034372,SRX21751585,SRS18859092,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X5 tp53het tumor,GSM7774461,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X5 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774461,GSM7774461: 19521X5 tp53het tumor; Danio rerio; RNA Seq,GSM7774461 r1,GSM7774461,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R1_001.fastq.gz 19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R2_001.fastq.gz,fastq fastq,18644081740.0,61735370.0,GSM7774461 r1,0:151 1:151,A:5198614433;C:4108657498;G:4307546758;T:5029072002;N:191049,151,151,,,5198614433,4108657498,4307546758,5029072002,191049,SRX21751585,SRS18859092,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.88544,0.88842,0.35896,0.35863,0.69193,0.69248,0.49682,0.50274,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26489,SRR26034373,SRX21751584,SRS18859091,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X4 tp53het tumor,GSM7774460,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X4 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774460,GSM7774460: 19521X4 tp53het tumor; Danio rerio; RNA Seq,GSM7774460 r1,GSM7774460,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R1_001.fastq.gz 19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R2_001.fastq.gz,fastq fastq,14417628886.0,47740493.0,GSM7774460 r1,0:151 1:151,A:4016299076;C:3183962020;G:3341158152;T:3876059438;N:150200,151,151,,,4016299076,3183962020,3341158152,3876059438,150200,SRX21751584,SRS18859091,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89118,0.89184,0.33812,0.33641,0.68947,0.68954,0.49867,0.50026,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26490,SRR26034374,SRX21751583,SRS18859090,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X3 tp53mut tumor,GSM7774459,,source name:brain|tissue:brain|tumor status:tumor|age:4 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X3 tp53mut tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:4 wpf|genotype:tp53 mutant,GSM7774459,GSM7774459: 19521X3 tp53mut tumor; Danio rerio; RNA Seq,GSM7774459 r1,GSM7774459,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X3_220211_A00421_0418_AHGVTMDSX3_S174_L003_R1_001.fastq.gz 19521X3_220211_A00421_0418_AHGVTMDSX3_S174_L003_R2_001.fastq.gz,fastq fastq,14792155696.0,48980648.0,GSM7774459 r1,0:151 1:151,A:4164614124;C:3233958816;G:3393302319;T:4000129008;N:151429,151,151,,,4164614124,3233958816,3393302319,4000129008,151429,SRX21751583,SRS18859090,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89303,0.8944,0.32883,0.32864,0.68024,0.68091,0.48335,0.48739,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Larval,Larval,Brain,Nervous System
26491,SRR26034375,SRX21751582,SRS18859089,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X2 tp53mut tumor,GSM7774458,,source name:brain|tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X2 tp53mut tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant,GSM7774458,GSM7774458: 19521X2 tp53mut tumor; Danio rerio; RNA Seq,GSM7774458 r1,GSM7774458,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R1_001.fastq.gz 19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R2_001.fastq.gz,fastq fastq,14064076580.0,46569790.0,GSM7774458 r1,0:151 1:151,A:3935649548;C:3089754695;G:3257286821;T:3781242542;N:142974,151,151,,,3935649548,3089754695,3257286821,3781242542,142974,SRX21751582,SRS18859089,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89595,0.89655,0.35454,0.35431,0.68927,0.69077,0.47888,0.47831,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26492,SRR26034376,SRX21751581,SRS18859088,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X1 tp53mut tumor,GSM7774457,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X1 tp53mut tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant,GSM7774457,GSM7774457: 19521X1 tp53mut tumor; Danio rerio; RNA Seq,GSM7774457 r1,GSM7774457,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R1_001.fastq.gz 19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R2_001.fastq.gz,fastq fastq,16911500190.0,55998345.0,GSM7774457 r1,0:151 1:151,A:4750241986;C:3698380612;G:3890633834;T:4572071732;N:172026,151,151,,,4750241986,3698380612,3890633834,4572071732,172026,SRX21751581,SRS18859088,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89695,0.89831,0.3562,0.35542,0.68392,0.68369,0.48172,0.48641,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
34192,SRR31443228,SRX26812023,SRS23296672,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 3,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 3,srrm4[y712] mutant replicate 3,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut3.pass2Aligned.sortedByCoord.out.bam,bam,23466336192.0,117587529.0,25938 mut3.pass2Aligned.sortedByCoord.out.bam,0:100.13 1:100.08,A:6298034402;C:5433884683;G:5344985734;T:6388443446;N:987927,100,100,,,6298034402,5433884683,5344985734,6388443446,987927,SRX26812023,SRS23296672,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.95864,0.95894,0.10681,0.1052,0.65385,0.65403,0.46511,0.46252,99,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34193,SRR31443229,SRX26812022,SRS23296671,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 3,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 3,srrm4[y712] wild type replicate 3,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt3.pass2Aligned.sortedByCoord.out.bam,bam,23979171134.0,120156039.0,25938 wt3.pass2Aligned.sortedByCoord.out.bam,0:100.12 1:100.07,A:6398807397;C:5589997524;G:5503127729;T:6486232627;N:1005857,100,100,,,6398807397,5589997524,5503127729,6486232627,1005857,SRX26812022,SRS23296671,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.95941,0.96004,0.10323,0.10191,0.65451,0.6532,0.46396,0.46398,101,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34194,SRR31443230,SRX26812021,SRS23296670,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 2,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 2,srrm4[y712] mutant replicate 2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut2.pass2Aligned.sortedByCoord.out.bam,bam,20256127500.0,101792067.0,25938 mut2.pass2Aligned.sortedByCoord.out.bam,0:100.05 1:100.00,A:5435798119;C:4683997479;G:4650293108;T:5485187428;N:851366,100,100,,,5435798119,4683997479,4650293108,5485187428,851366,SRX26812021,SRS23296670,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.96008,0.96049,0.10232,0.10156,0.66072,0.65932,0.4668,0.46817,95,95,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34195,SRR31443231,SRX26812020,SRS23296669,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 2,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 2,srrm4[y712] wild type replicate 2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt2.pass2Aligned.sortedByCoord.out.bam,bam,22698373371.0,113599687.0,25938 wt2.pass2Aligned.sortedByCoord.out.bam,0:100.18 1:100.12,A:6063922145;C:5275724786;G:5212055837;T:6145709475;N:961128,100,100,,,6063922145,5275724786,5212055837,6145709475,961128,SRX26812020,SRS23296669,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.96129,0.96063,0.1003,0.09861,0.65744,0.65748,0.46167,0.46817,98,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34196,SRR31443232,SRX26812019,SRS23296667,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 1,,strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 1,srrm4[y712] mutant replicate 1,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut.pass2Aligned.sortedByCoord.out.bam,bam,11282501509.0,56702666.0,25938 mut.pass2Aligned.sortedByCoord.out.bam,0:99.65 1:99.55,A:2764745971;C:2868447715;G:2856237429;T:2792914545;N:155849,99,99,,,2764745971,2868447715,2856237429,2792914545,155849,SRX26812019,SRS23296667,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34197,SRR31443233,SRX26812018,SRS23296668,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 1,,strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 1,srrm4[y712] wild type replicate 1,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt.pass2Aligned.sortedByCoord.out.bam,bam,16346812838.0,82104499.0,25938 wt.pass2Aligned.sortedByCoord.out.bam,0:99.65 1:99.56,A:3996717287;C:4167381503;G:4130586142;T:4051899914;N:227992,99,99,,,3996717287,4167381503,4130586142,4051899914,227992,SRX26812018,SRS23296668,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.97776,0.97907,0.04095,0.04006,0.6702,0.67034,0.46611,0.46144,99,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34945,SRR32472665,SRX27787001,SRS24165038,SRP565999,PRJNA1227535,Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3,GSE290354,Transcriptome Analysis,Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3  and despite its severe clinical presentation  currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier  we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However  starting by 10 dpf  mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination  changes reminiscent of the nerve pathology in human CMT4B3. Importantly  RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis  chromatin remodeling/organization  and synaptic membrane homeostasis. Overall  our mtmr5 knockout zebrafish mirror genetic  clinical  and pathologic features of human CMT4B3. As such  it represents a first pre clinical model to phenocopy the disease  and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.,,pubmed:40066109,,Brain enriched  mtmr5 knockout  biol rep4,GSM8811137,,source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing,Brain enriched  mtmr5 knockout  biol rep4,Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection   nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly  downloaded on October 21  2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples,head,,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children  Toronto  ON  Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean  1 mg/L methylene blue  pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.,tissue:head|genotype:mtmr5 knockout,GSM8811137,GSM8811137: Brain enriched  mtmr5 knockout  biol rep4; Danio rerio; RNA Seq,GSM8811137 r1,GSM8811137,1,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP565999,,,mtmr5_KO_4_S45_L002_R1_001.fastq.gz mtmr5_KO_4_S45_L002_R2_001.fastq.gz,fastq fastq,10453259182.0,34613441.0,GSM8811137 r1,0:151 1:151,A:3266219433;C:1966251945;G:2032163425;T:3188611188;N:13191,151,151,,,3266219433,1966251945,2032163425,3188611188,13191,SRX27787001,SRS24165038,SRA2083091,"Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning","Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Canada,2025-02-24,Larval,Larval,Head,Nervous System
34946,SRR32472666,SRX27787000,SRS24165036,SRP565999,PRJNA1227535,Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3,GSE290354,Transcriptome Analysis,Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3  and despite its severe clinical presentation  currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier  we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However  starting by 10 dpf  mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination  changes reminiscent of the nerve pathology in human CMT4B3. Importantly  RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis  chromatin remodeling/organization  and synaptic membrane homeostasis. Overall  our mtmr5 knockout zebrafish mirror genetic  clinical  and pathologic features of human CMT4B3. As such  it represents a first pre clinical model to phenocopy the disease  and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.,,pubmed:40066109,,Brain enriched  mtmr5 knockout  biol rep3,GSM8811136,,source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing,Brain enriched  mtmr5 knockout  biol rep3,Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection   nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly  downloaded on October 21  2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples,head,,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children  Toronto  ON  Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean  1 mg/L methylene blue  pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.,tissue:head|genotype:mtmr5 knockout,GSM8811136,GSM8811136: Brain enriched  mtmr5 knockout  biol rep3; Danio rerio; RNA Seq,GSM8811136 r1,GSM8811136,1,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP565999,,,mtmr5_KO_3_S43_L002_R1_001.fastq.gz mtmr5_KO_3_S43_L002_R2_001.fastq.gz,fastq fastq,12084666202.0,40015451.0,GSM8811136 r1,0:151 1:151,A:3753711310;C:2294198185;G:2375272418;T:3661468451;N:15838,151,151,,,3753711310,2294198185,2375272418,3661468451,15838,SRX27787000,SRS24165036,SRA2083091,"Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning","Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Canada,2025-02-24,Larval,Larval,Head,Nervous System
34947,SRR32472667,SRX27786999,SRS24165037,SRP565999,PRJNA1227535,Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3,GSE290354,Transcriptome Analysis,Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3  and despite its severe clinical presentation  currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier  we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However  starting by 10 dpf  mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination  changes reminiscent of the nerve pathology in human CMT4B3. Importantly  RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis  chromatin remodeling/organization  and synaptic membrane homeostasis. Overall  our mtmr5 knockout zebrafish mirror genetic  clinical  and pathologic features of human CMT4B3. As such  it represents a first pre clinical model to phenocopy the disease  and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.,,pubmed:40066109,,Brain enriched  mtmr5 knockout  biol rep2,GSM8811135,,source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing,Brain enriched  mtmr5 knockout  biol rep2,Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection   nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly  downloaded on October 21  2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples,head,,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children  Toronto  ON  Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean  1 mg/L methylene blue  pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.,tissue:head|genotype:mtmr5 knockout,GSM8811135,GSM8811135: Brain enriched  mtmr5 knockout  biol rep2; Danio rerio; RNA Seq,GSM8811135 r1,GSM8811135,1,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP565999,,,mtmr5_KO_2_S41_L002_R1_001.fastq.gz mtmr5_KO_2_S41_L002_R2_001.fastq.gz,fastq fastq,11376848568.0,37671684.0,GSM8811135 r1,0:151 1:151,A:3528535891;C:2164674917;G:2231865046;T:3451757695;N:15019,151,151,,,3528535891,2164674917,2231865046,3451757695,15019,SRX27786999,SRS24165037,SRA2083091,"Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning","Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Canada,2025-02-24,Larval,Larval,Head,Nervous System
34948,SRR32472668,SRX27786998,SRS24165034,SRP565999,PRJNA1227535,Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3,GSE290354,Transcriptome Analysis,Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3  and despite its severe clinical presentation  currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier  we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However  starting by 10 dpf  mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination  changes reminiscent of the nerve pathology in human CMT4B3. Importantly  RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis  chromatin remodeling/organization  and synaptic membrane homeostasis. Overall  our mtmr5 knockout zebrafish mirror genetic  clinical  and pathologic features of human CMT4B3. As such  it represents a first pre clinical model to phenocopy the disease  and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.,,pubmed:40066109,,Brain enriched  mtmr5 knockout  biol rep1,GSM8811134,,source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing,Brain enriched  mtmr5 knockout  biol rep1,Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection   nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly  downloaded on October 21  2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples,head,,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children  Toronto  ON  Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean  1 mg/L methylene blue  pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.,tissue:head|genotype:mtmr5 knockout,GSM8811134,GSM8811134: Brain enriched  mtmr5 knockout  biol rep1; Danio rerio; RNA Seq,GSM8811134 r1,GSM8811134,1,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP565999,,,mtmr5_KO_1_S39_L002_R1_001.fastq.gz mtmr5_KO_1_S39_L002_R2_001.fastq.gz,fastq fastq,10620109350.0,35165925.0,GSM8811134 r1,0:151 1:151,A:3306163050;C:2008249825;G:2075153541;T:3230528981;N:13953,151,151,,,3306163050,2008249825,2075153541,3230528981,13953,SRX27786998,SRS24165034,SRA2083091,"Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning","Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Canada,2025-02-24,Larval,Larval,Head,Nervous System
34949,SRR32472669,SRX27786997,SRS24165033,SRP565999,PRJNA1227535,Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3,GSE290354,Transcriptome Analysis,Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3  and despite its severe clinical presentation  currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier  we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However  starting by 10 dpf  mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination  changes reminiscent of the nerve pathology in human CMT4B3. Importantly  RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis  chromatin remodeling/organization  and synaptic membrane homeostasis. Overall  our mtmr5 knockout zebrafish mirror genetic  clinical  and pathologic features of human CMT4B3. As such  it represents a first pre clinical model to phenocopy the disease  and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.,,pubmed:40066109,,Brain enriched  wild type  biol rep4,GSM8811133,,source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing,Brain enriched  wild type  biol rep4,Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection   nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly  downloaded on October 21  2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples,head,,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children  Toronto  ON  Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean  1 mg/L methylene blue  pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.,tissue:head|genotype:wild type,GSM8811133,GSM8811133: Brain enriched  wild type  biol rep4; Danio rerio; RNA Seq,GSM8811133 r1,GSM8811133,1,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP565999,,,mtmr5_WT_4_S44_L002_R1_001.fastq.gz mtmr5_WT_4_S44_L002_R2_001.fastq.gz,fastq fastq,12990872770.0,43016135.0,GSM8811133 r1,0:151 1:151,A:3923529419;C:2571621367;G:2649969483;T:3845735356;N:17145,151,151,,,3923529419,2571621367,2649969483,3845735356,17145,SRX27786997,SRS24165033,SRA2083091,"Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning","Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning",2,0.89808,0.89653,0.27845,0.2761,0.74479,0.74412,0.52081,0.52503,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Canada,2025-02-24,Larval,Larval,Head,Nervous System
34950,SRR32472670,SRX27786996,SRS24165032,SRP565999,PRJNA1227535,Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3,GSE290354,Transcriptome Analysis,Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3  and despite its severe clinical presentation  currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier  we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However  starting by 10 dpf  mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination  changes reminiscent of the nerve pathology in human CMT4B3. Importantly  RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis  chromatin remodeling/organization  and synaptic membrane homeostasis. Overall  our mtmr5 knockout zebrafish mirror genetic  clinical  and pathologic features of human CMT4B3. As such  it represents a first pre clinical model to phenocopy the disease  and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.,,pubmed:40066109,,Brain enriched  wild type  biol rep3,GSM8811132,,source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing,Brain enriched  wild type  biol rep3,Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection   nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly  downloaded on October 21  2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples,head,,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children  Toronto  ON  Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean  1 mg/L methylene blue  pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.,tissue:head|genotype:wild type,GSM8811132,GSM8811132: Brain enriched  wild type  biol rep3; Danio rerio; RNA Seq,GSM8811132 r1,GSM8811132,1,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP565999,,,mtmr5_WT_3_S42_L002_R1_001.fastq.gz mtmr5_WT_3_S42_L002_R2_001.fastq.gz,fastq fastq,11980025618.0,39668959.0,GSM8811132 r1,0:151 1:151,A:3620876130;C:2376508941;G:2435934723;T:3546690015;N:15809,151,151,,,3620876130,2376508941,2435934723,3546690015,15809,SRX27786996,SRS24165032,SRA2083091,"Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning","Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Canada,2025-02-24,Larval,Larval,Head,Nervous System
34951,SRR32472671,SRX27786995,SRS24165035,SRP565999,PRJNA1227535,Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3,GSE290354,Transcriptome Analysis,Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3  and despite its severe clinical presentation  currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier  we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However  starting by 10 dpf  mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination  changes reminiscent of the nerve pathology in human CMT4B3. Importantly  RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis  chromatin remodeling/organization  and synaptic membrane homeostasis. Overall  our mtmr5 knockout zebrafish mirror genetic  clinical  and pathologic features of human CMT4B3. As such  it represents a first pre clinical model to phenocopy the disease  and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.,,pubmed:40066109,,Brain enriched  wild type  biol rep2,GSM8811131,,source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing,Brain enriched  wild type  biol rep2,Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection   nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly  downloaded on October 21  2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples,head,,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children  Toronto  ON  Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean  1 mg/L methylene blue  pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.,tissue:head|genotype:wild type,GSM8811131,GSM8811131: Brain enriched  wild type  biol rep2; Danio rerio; RNA Seq,GSM8811131 r1,GSM8811131,1,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP565999,,,mtmr5_WT_2_S40_L002_R1_001.fastq.gz mtmr5_WT_2_S40_L002_R2_001.fastq.gz,fastq fastq,12148102812.0,40225506.0,GSM8811131 r1,0:151 1:151,A:3574846721;C:2501278590;G:2563116243;T:3508845082;N:16176,151,151,,,3574846721,2501278590,2563116243,3508845082,16176,SRX27786995,SRS24165035,SRA2083091,"Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning","Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Canada,2025-02-24,Larval,Larval,Head,Nervous System
34952,SRR32472672,SRX27786994,SRS24165031,SRP565999,PRJNA1227535,Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3,GSE290354,Transcriptome Analysis,Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3  and despite its severe clinical presentation  currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier  we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However  starting by 10 dpf  mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination  changes reminiscent of the nerve pathology in human CMT4B3. Importantly  RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis  chromatin remodeling/organization  and synaptic membrane homeostasis. Overall  our mtmr5 knockout zebrafish mirror genetic  clinical  and pathologic features of human CMT4B3. As such  it represents a first pre clinical model to phenocopy the disease  and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.,,pubmed:40066109,,Brain enriched  wild type  biol rep1,GSM8811130,,source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing,Brain enriched  wild type  biol rep1,Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection   nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly  downloaded on October 21  2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples,head,,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children  Toronto  ON  Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean  1 mg/L methylene blue  pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.,tissue:head|genotype:wild type,GSM8811130,GSM8811130: Brain enriched  wild type  biol rep1; Danio rerio; RNA Seq,GSM8811130 r1,GSM8811130,1,Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf  n=11 17 zebrafish heads were dissected per genotype  and immediately frozen at  80C. RNA extraction was performed for all samples 4x WT  and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control  RNA library preparation  cDNA synthesis  and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP565999,,,mtmr5_WT_1_S38_L002_R1_001.fastq.gz mtmr5_WT_1_S38_L002_R2_001.fastq.gz,fastq fastq,12280050236.0,40662418.0,GSM8811130 r1,0:151 1:151,A:3666524090;C:2479893988;G:2540363922;T:3593251867;N:16369,151,151,,,3666524090,2479893988,2540363922,3593251867,16369,SRX27786994,SRS24165031,SRA2083091,"Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning","Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning",2,0.91363,0.9138,0.2442,0.24267,0.72232,0.72123,0.47864,0.53039,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Canada,2025-02-24,Larval,Larval,Head,Nervous System
53495,SRR9886611,SRX6639067,SRS5209782,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000,,pubmed:32859696,,GH6,GSM4002525,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1  / ,GH6,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample,Brain,,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf dj 1  / ,GSM4002525,GSM4002525: GH6; Danio rerio; RNA Seq,GSM4002525,,1,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002525,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH6_S41_L004_R1_001.fastq-004.gz GH6_S41_L004_R2_001.fastq-009.gz,fastq fastq,16197223984.0,53633192.0,GSM4002525 r1,0:151 1:151,A:4524520245;C:3580881754;G:3728671047;T:4362276906;N:874032,151,151,,,4524520245,3580881754,3728671047,4362276906,874032,SRX6639067,SRS5209782,SRA931013,GEO,"Biology, University of York",2,0.91745,0.9163,0.15171,0.14974,0.69826,0.70161,0.49509,0.48979,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53496,SRR9886610,SRX6639066,SRS5209781,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000,,pubmed:32859696,,GH5,GSM4002524,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1  / ,GH5,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample,Brain,,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf dj 1  / ,GSM4002524,GSM4002524: GH5; Danio rerio; RNA Seq,GSM4002524,,1,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002524,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH5_S40_L004_R1_001.fastq-001.gz GH5_S40_L004_R2_001.fastq-003.gz,fastq fastq,14762621304.0,48882852.0,GSM4002524 r1,0:151 1:151,A:4134788753;C:3245817056;G:3388258601;T:3992937107;N:819787,151,151,,,4134788753,3245817056,3388258601,3992937107,819787,SRX6639066,SRS5209781,SRA931013,GEO,"Biology, University of York",2,0.91356,0.91354,0.15637,0.15448,0.69755,0.70177,0.48873,0.49642,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53497,SRR9886609,SRX6639065,SRS5209780,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000,,pubmed:32859696,,GH4,GSM4002523,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1  / ,GH4,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample,Brain,,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf dj 1  / ,GSM4002523,GSM4002523: GH4; Danio rerio; RNA Seq,GSM4002523,,1,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002523,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH4_S39_L004_R1_001.fastq-008.gz GH4_S39_L004_R2_001.fastq-011.gz,fastq fastq,17232418376.0,57060988.0,GSM4002523 r1,0:151 1:151,A:4798343141;C:3812370940;G:3947002545;T:4673748329;N:953421,151,151,,,4798343141,3812370940,3947002545,4673748329,953421,SRX6639065,SRS5209780,SRA931013,GEO,"Biology, University of York",2,0.91359,0.91289,0.15791,0.15599,0.70128,0.70585,0.48423,0.48897,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53498,SRR9886608,SRX6639064,SRS5209779,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000,,pubmed:32859696,,GH3,GSM4002522,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type,GH3,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample,Brain,,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf type,GSM4002522,GSM4002522: GH3; Danio rerio; RNA Seq,GSM4002522,,1,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002522,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH3_S38_L004_R1_001.fastq-002.gz GH3_S38_L004_R2_001.fastq-005.gz,fastq fastq,15880659430.0,52584965.0,GSM4002522 r1,0:151 1:151,A:4428460730;C:3500855291;G:3647161094;T:4303300463;N:881852,151,151,,,4428460730,3500855291,3647161094,4303300463,881852,SRX6639064,SRS5209779,SRA931013,GEO,"Biology, University of York",2,0.91311,0.91404,0.15734,0.15592,0.69621,0.70092,0.4936,0.48217,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53499,SRR9886607,SRX6639063,SRS5209778,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000,,pubmed:32859696,,GH2,GSM4002521,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type,GH2,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample,Brain,,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf type,GSM4002521,GSM4002521: GH2; Danio rerio; RNA Seq,GSM4002521,,1,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002521,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH2_S37_L004_R1_001.fastq-006.gz GH2_S37_L004_R2_001.fastq-012.gz,fastq fastq,17721573816.0,58680708.0,GSM4002521 r1,0:151 1:151,A:4948184152;C:3901958410;G:4066182263;T:4804260891;N:988100,151,151,,,4948184152,3901958410,4066182263,4804260891,988100,SRX6639063,SRS5209778,SRA931013,GEO,"Biology, University of York",2,0.90975,0.90966,0.16242,0.16044,0.69934,0.70339,0.48497,0.49335,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53500,SRR9886606,SRX6639062,SRS5209777,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 /  zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 /  mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1  /  zebrafish were generated by deep sequencing  in triplicate  using Illumina HiSeq 3000,,pubmed:32859696,,GH1,GSM4002520,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type,GH1,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript  hypertext markup language document including read counts per sample,Brain,,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf type,GSM4002520,GSM4002520: GH1; Danio rerio; RNA Seq,GSM4002520,,1,Brains were removed  flash frozen in liquid nitrogen  and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002520,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH1_S36_L004_R1_001.fastq-007.gz GH1_S36_L004_R2_001.fastq-010.gz,fastq fastq,16852076254.0,55801577.0,GSM4002520 r1,0:151 1:151,A:4697089825;C:3744087924;G:3878965083;T:4531030410;N:903012,151,151,,,4697089825,3744087924,3878965083,4531030410,903012,SRX6639062,SRS5209777,SRA931013,GEO,"Biology, University of York",2,0.91719,0.91765,0.15136,0.15011,0.69998,0.70455,0.48284,0.48335,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
56512,SRR10988549,SRX7649999,SRS6079496,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib3,GSM4289907,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib3,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289907,GSM4289907: head  2d rw440 sib3; Danio rerio; RNA Seq,GSM4289907,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289907,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib3_R2.fastq.gz 2d_rw440_sib3_R1.fastq.gz,fastq fastq,3140682329.0,10457484.0,GSM4289907 r1,0:150.21 1:150.12,A:760684292;C:777389008;G:783922642;T:818121129;N:565258,150,150,,,760684292,777389008,783922642,818121129,565258,SRX7649999,SRS6079496,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93527,0.95251,0.03293,0.02826,0.72032,0.73669,0.4787,0.47899,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56513,SRR10988548,SRX7649998,SRS6079495,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib2,GSM4289906,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib2,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289906,GSM4289906: head  2d rw440 sib2; Danio rerio; RNA Seq,GSM4289906,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289906,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib2_R1.fastq.gz 2d_rw440_sib2_R2.fastq.gz,fastq fastq,3194598681.0,10634398.0,GSM4289906 r1,0:150.24 1:150.17,A:771547062;C:789590364;G:796831526;T:835985747;N:643982,150,150,,,771547062,789590364,796831526,835985747,643982,SRX7649998,SRS6079495,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93377,0.95416,0.02628,0.02182,0.72989,0.74805,0.46631,0.47654,149,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56514,SRR10988547,SRX7649997,SRS6079494,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib1,GSM4289905,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib1,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289905,GSM4289905: head  2d rw440 sib1; Danio rerio; RNA Seq,GSM4289905,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289905,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib1_R1.fastq.gz 2d_rw440_sib1_R2.fastq.gz,fastq fastq,2654979688.0,8840507.0,GSM4289905 r1,0:150.19 1:150.13,A:624000299;C:675145222;G:678635011;T:676731946;N:467210,150,150,,,624000299,675145222,678635011,676731946,467210,SRX7649997,SRS6079494,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.9317,0.94861,0.06364,0.05753,0.72811,0.75055,0.50771,0.52256,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56515,SRR10988546,SRX7649996,SRS6079493,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut3,GSM4289904,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut3,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289904,GSM4289904: head  2d rw440 mut3; Danio rerio; RNA Seq,GSM4289904,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289904,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut3_R1.fastq.gz 2d_rw440_mut3_R2.fastq.gz,fastq fastq,3282506507.0,10958106.0,GSM4289904 r1,0:149.81 1:149.74,A:781014809;C:816143245;G:824711112;T:858035111;N:2602230,149,149,,,781014809,816143245,824711112,858035111,2602230,SRX7649996,SRS6079493,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93293,0.95901,0.02641,0.023,0.74408,0.76449,0.48032,0.475,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56516,SRR10988545,SRX7649995,SRS6079492,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut2,GSM4289903,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut2,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289903,GSM4289903: head  2d rw440 mut2; Danio rerio; RNA Seq,GSM4289903,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289903,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut2_R2.fastq.gz 2d_rw440_mut2_R1.fastq.gz,fastq fastq,2673347852.0,8908620.0,GSM4289903 r1,0:150.07 1:150.01,A:641733072;C:667262119;G:672992510;T:690242042;N:1118109,150,150,,,641733072,667262119,672992510,690242042,1118109,SRX7649995,SRS6079492,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93754,0.95755,0.03962,0.0352,0.72234,0.73963,0.47668,0.49072,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56517,SRR10988544,SRX7649994,SRS6079491,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut1,GSM4289902,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut1,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289902,GSM4289902: head  2d rw440 mut1; Danio rerio; RNA Seq,GSM4289902,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289902,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut1_R1.fastq.gz 2d_rw440_mut1_R2.fastq.gz,fastq fastq,2609801785.0,8695280.0,GSM4289902 r1,0:150.10 1:150.04,A:629026157;C:649393814;G:654616712;T:676204104;N:560998,150,150,,,629026157,649393814,654616712,676204104,560998,SRX7649994,SRS6079491,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93478,0.95296,0.02959,0.0259,0.72458,0.74209,0.4765,0.47804,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
65793,SRR15626575,SRX11923642,SRS9937160,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 C5,GSM5538904,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury,W6 C5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury,GSM5538904,GSM5538904: W6 C5; Danio rerio; RNA Seq,GSM5538904,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538904,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_C5_1.fq.gz W6_C5_2.fq.gz,fastq fastq,11548053600.0,38493512.0,GSM5538904 r1,0:150 1:150,A:3284639772;C:2417614008;G:2424125351;T:3421247186;N:427283,150,150,,,3284639772,2417614008,2424125351,3421247186,427283,SRX11923642,SRS9937160,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92424,0.91753,0.09206,0.08921,0.73817,0.75006,0.48669,0.46123,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65794,SRR15626574,SRX11923641,SRS9937158,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 C3,GSM5538903,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury,W6 C3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury,GSM5538903,GSM5538903: W6 C3; Danio rerio; RNA Seq,GSM5538903,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538903,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_C3_1.fq.gz W6_C3_2.fq.gz,fastq fastq,8675036411.0,29294039.0,GSM5538903 r1,,A:2490417531;C:1754549667;G:1762976045;T:2666940038;N:153130,,,,,2490417531,1754549667,1762976045,2666940038,153130,SRX11923641,SRS9937158,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.77214,0.76518,0.16042,0.15604,0.72425,0.74251,0.47844,0.47263,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65795,SRR15626573,SRX11923640,SRS9937159,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 C2,GSM5538902,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury,W6 C2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury,GSM5538902,GSM5538902: W6 C2; Danio rerio; RNA Seq,GSM5538902,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538902,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_C2_1.fq.gz W6_C2_2.fq.gz,fastq fastq,10539241978.0,35799607.0,GSM5538902 r1,,A:2981919265;C:2108326349;G:2140188676;T:3307713377;N:1094311,,,,,2981919265,2108326349,2140188676,3307713377,1094311,SRX11923640,SRS9937159,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.79298,0.77869,0.15756,0.14594,0.71504,0.73527,0.52219,0.3777,126,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65796,SRR15626572,SRX11923639,SRS9937157,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 C1,GSM5538901,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury,W6 C1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury,GSM5538901,GSM5538901: W6 C1; Danio rerio; RNA Seq,GSM5538901,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538901,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_C1_1.fq.gz W6_C1_2.fq.gz,fastq fastq,10943049099.0,37073140.0,GSM5538901 r1,,A:3130283377;C:2198486300;G:2220073292;T:3393075128;N:1131002,,,,,3130283377,2198486300,2220073292,3393075128,1131002,SRX11923639,SRS9937157,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.80382,0.80796,0.16342,0.16071,0.72275,0.73456,0.49635,0.49821,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65797,SRR15626571,SRX11923638,SRS9937156,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 R5,GSM5538900,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,W6 R5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,GSM5538900,GSM5538900: W6 R5; Danio rerio; RNA Seq,GSM5538900,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538900,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_R5_1.fq.gz W6_R5_2.fq.gz,fastq fastq,12204896100.0,40682987.0,GSM5538900 r1,0:150 1:150,A:3461249396;C:2529425680;G:2571904738;T:3640345896;N:1970390,150,150,,,3461249396,2529425680,2571904738,3640345896,1970390,SRX11923638,SRS9937156,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.91134,0.91584,0.10821,0.10746,0.73588,0.75207,0.52657,0.48765,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65798,SRR15626570,SRX11923637,SRS9937155,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 R4,GSM5538899,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,W6 R4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,GSM5538899,GSM5538899: W6 R4; Danio rerio; RNA Seq,GSM5538899,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538899,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_R4_1.fq.gz W6_R4_2.fq.gz,fastq fastq,11563962300.0,38546541.0,GSM5538899 r1,0:150 1:150,A:3303789178;C:2399710240;G:2415791330;T:3443551642;N:1119910,150,150,,,3303789178,2399710240,2415791330,3443551642,1119910,SRX11923637,SRS9937155,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.91143,0.90985,0.11486,0.11393,0.73825,0.74533,0.54532,0.52817,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65799,SRR15626569,SRX11923636,SRS9937154,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 R3,GSM5538898,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,W6 R3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,GSM5538898,GSM5538898: W6 R3; Danio rerio; RNA Seq,GSM5538898,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538898,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_R3_1.fq.gz W6_R3_2.fq.gz,fastq fastq,10585954542.0,35816604.0,GSM5538898 r1,,A:3037575766;C:2127628123;G:2139476709;T:3281099271;N:174673,,,,,3037575766,2127628123,2139476709,3281099271,174673,SRX11923636,SRS9937154,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.85058,0.85296,0.1621,0.15714,0.71713,0.73582,0.52255,0.50069,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65800,SRR15626568,SRX11923635,SRS9937153,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 R2,GSM5538897,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,W6 R2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,GSM5538897,GSM5538897: W6 R2; Danio rerio; RNA Seq,GSM5538897,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538897,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_R2_1.fq.gz W6_R2_2.fq.gz,fastq fastq,10669861075.0,36260298.0,GSM5538897 r1,,A:3008779806;C:2132058614;G:2164237979;T:3363597660;N:1187016,,,,,3008779806,2132058614,2164237979,3363597660,1187016,SRX11923635,SRS9937153,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.80233,0.78844,0.14557,0.1354,0.7179,0.73914,0.50279,0.38358,150,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65801,SRR15626567,SRX11923634,SRS9937152,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W6 R1,GSM5538896,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,W6 R1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury,GSM5538896,GSM5538896: W6 R1; Danio rerio; RNA Seq,GSM5538896,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538896,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W6_R1_1.fq.gz W6_R1_2.fq.gz,fastq fastq,8919305763.0,30118529.0,GSM5538896 r1,,A:2544200186;C:1819461355;G:1834522593;T:2720239204;N:882425,,,,,2544200186,1819461355,1834522593,2720239204,882425,SRX11923634,SRS9937152,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.81775,0.81798,0.17053,0.16924,0.7161,0.72971,0.50177,0.49561,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65802,SRR15626566,SRX11923633,SRS9937151,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 C5,GSM5538895,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,W4 C5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,GSM5538895,GSM5538895: W4 C5; Danio rerio; RNA Seq,GSM5538895,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538895,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_C5_1.fq.gz W4_C5_2.fq.gz,fastq fastq,11543122500.0,38477075.0,GSM5538895 r1,0:150 1:150,A:3264584729;C:2405081333;G:2441204011;T:3430418662;N:1833765,150,150,,,3264584729,2405081333,2441204011,3430418662,1833765,SRX11923633,SRS9937151,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.91535,0.91481,0.10079,0.09867,0.73671,0.75333,0.497,0.47606,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65803,SRR15626565,SRX11923632,SRS9937150,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 C4,GSM5538894,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,W4 C4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,GSM5538894,GSM5538894: W4 C4; Danio rerio; RNA Seq,GSM5538894,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538894,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_C4_1.fq.gz W4_C4_2.fq.gz,fastq fastq,12129480900.0,40431603.0,GSM5538894 r1,0:150 1:150,A:3451519288;C:2515952240;G:2531389661;T:3629453781;N:1165930,150,150,,,3451519288,2515952240,2531389661,3629453781,1165930,SRX11923632,SRS9937150,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.90598,0.90619,0.11287,0.10949,0.74184,0.75049,0.52714,0.51794,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65804,SRR15626564,SRX11923631,SRS9937149,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 C3,GSM5538893,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,W4 C3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,GSM5538893,GSM5538893: W4 C3; Danio rerio; RNA Seq,GSM5538893,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538893,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_C3_1.fq.gz W4_C3_2.fq.gz,fastq fastq,14082618084.0,47123575.0,GSM5538893 r1,,A:4015557919;C:3022962754;G:2997180467;T:4041325245;N:5591699,,,,,4015557919,3022962754,2997180467,4041325245,5591699,SRX11923631,SRS9937149,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92908,0.92957,0.15754,0.15803,0.6929,0.70116,0.47235,0.46006,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65805,SRR15626563,SRX11923630,SRS9937148,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 C2,GSM5538892,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,W4 C2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,GSM5538892,GSM5538892: W4 C2; Danio rerio; RNA Seq,GSM5538892,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538892,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_C2_1.fq.gz W4_C2_2.fq.gz,fastq fastq,9869014911.0,33378223.0,GSM5538892 r1,,A:2804174507;C:2004352577;G:2027844843;T:3031342717;N:1300267,,,,,2804174507,2004352577,2027844843,3031342717,1300267,SRX11923630,SRS9937148,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.74408,0.76084,0.15302,0.15477,0.71871,0.72863,0.41139,0.49828,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65806,SRR15626562,SRX11923629,SRS9937147,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 C1,GSM5538891,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,W4 C1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury,GSM5538891,GSM5538891: W4 C1; Danio rerio; RNA Seq,GSM5538891,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538891,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_C1_1.fq.gz W4_C1_2.fq.gz,fastq fastq,10687932882.0,36203087.0,GSM5538891 r1,,A:3008283529;C:2182572792;G:2209894531;T:3285549998;N:1632032,,,,,3008283529,2182572792,2209894531,3285549998,1632032,SRX11923629,SRS9937147,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.78654,0.7865,0.12675,0.12286,0.71973,0.73154,0.48571,0.48208,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65807,SRR15626561,SRX11923628,SRS9937146,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 R5,GSM5538890,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,W4 R5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,GSM5538890,GSM5538890: W4 R5; Danio rerio; RNA Seq,GSM5538890,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538890,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_R5_1.fq.gz W4_R5_2.fq.gz,fastq fastq,10826625600.0,36088752.0,GSM5538890 r1,0:150 1:150,A:3070709719;C:2256203149;G:2290582547;T:3207400991;N:1729194,150,150,,,3070709719,2256203149,2290582547,3207400991,1729194,SRX11923628,SRS9937146,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92731,0.92152,0.09349,0.09234,0.74298,0.75749,0.51393,0.5062,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65808,SRR15626560,SRX11923627,SRS9937144,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 R4,GSM5538889,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,W4 R4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,GSM5538889,GSM5538889: W4 R4; Danio rerio; RNA Seq,GSM5538889,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538889,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_R4_1.fq.gz W4_R4_2.fq.gz,fastq fastq,12376562700.0,41255209.0,GSM5538889 r1,0:150 1:150,A:3541278294;C:2530972782;G:2556584213;T:3745659123;N:2068288,150,150,,,3541278294,2530972782,2556584213,3745659123,2068288,SRX11923627,SRS9937144,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.89512,0.89467,0.10934,0.10598,0.7501,0.76045,0.55625,0.53279,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65809,SRR15626559,SRX11923626,SRS9937145,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 R3,GSM5538888,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,W4 R3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,GSM5538888,GSM5538888: W4 R3; Danio rerio; RNA Seq,GSM5538888,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538888,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_R3_1.fq.gz W4_R3_2.fq.gz,fastq fastq,12994033001.0,43618576.0,GSM5538888 r1,,A:3734612575;C:2723842641;G:2695083832;T:3835271719;N:5222234,,,,,3734612575,2723842641,2695083832,3835271719,5222234,SRX11923626,SRS9937145,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92675,0.92704,0.17531,0.17471,0.71407,0.72421,0.49948,0.49784,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65810,SRR15626558,SRX11923625,SRS9937143,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 R2,GSM5538887,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,W4 R2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,GSM5538887,GSM5538887: W4 R2; Danio rerio; RNA Seq,GSM5538887,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538887,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_R2_1.fq.gz W4_R2_2.fq.gz,fastq fastq,9939535918.0,33661519.0,GSM5538887 r1,,A:2798350929;C:2035721017;G:2056764740;T:3047330104;N:1369128,,,,,2798350929,2035721017,2056764740,3047330104,1369128,SRX11923625,SRS9937143,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.83192,0.82813,0.14852,0.14323,0.70822,0.7247,0.5042,0.39639,150,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65811,SRR15626557,SRX11923624,SRS9937142,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W4 R1,GSM5538886,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,W4 R1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury,GSM5538886,GSM5538886: W4 R1; Danio rerio; RNA Seq,GSM5538886,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538886,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W4_R1_1.fq.gz W4_R1_2.fq.gz,fastq fastq,11296616614.0,38212724.0,GSM5538886 r1,,A:3243016820;C:2270852137;G:2299184572;T:3481964410;N:1598675,,,,,3243016820,2270852137,2299184572,3481964410,1598675,SRX11923624,SRS9937142,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.82944,0.83777,0.17869,0.17723,0.71887,0.72855,0.55802,0.54964,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65812,SRR15626556,SRX11923623,SRS9937141,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 C5,GSM5538885,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,W2 C5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,GSM5538885,GSM5538885: W2 C5; Danio rerio; RNA Seq,GSM5538885,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538885,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_C5_1.fq.gz W2_C5_2.fq.gz,fastq fastq,12070135500.0,40233785.0,GSM5538885 r1,0:150 1:150,A:3401996219;C:2534578869;G:2548303668;T:3583247357;N:2009387,150,150,,,3401996219,2534578869,2548303668,3583247357,2009387,SRX11923623,SRS9937141,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.9072,0.90232,0.11716,0.11618,0.72636,0.73685,0.5018,0.49535,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65813,SRR15626555,SRX11923622,SRS9937139,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 C4,GSM5538884,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,W2 C4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,GSM5538884,GSM5538884: W2 C4; Danio rerio; RNA Seq,GSM5538884,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538884,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_C4_1.fq.gz W2_C4_2.fq.gz,fastq fastq,10594271400.0,35314238.0,GSM5538884 r1,0:150 1:150,A:2987614251;C:2191740653;G:2212201491;T:3200908482;N:1806523,150,150,,,2987614251,2191740653,2212201491,3200908482,1806523,SRX11923622,SRS9937139,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.91565,0.91107,0.10017,0.09553,0.74253,0.7543,0.57884,0.57058,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65814,SRR15626554,SRX11923621,SRS9937140,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 C3,GSM5538883,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,W2 C3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,GSM5538883,GSM5538883: W2 C3; Danio rerio; RNA Seq,GSM5538883,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538883,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_C3_1.fq.gz W2_C3_2.fq.gz,fastq fastq,13355624941.0,44841516.0,GSM5538883 r1,,A:3801123201;C:2832441023;G:2806117424;T:3910715830;N:5227463,,,,,3801123201,2832441023,2806117424,3910715830,5227463,SRX11923621,SRS9937140,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.93011,0.93014,0.14881,0.1487,0.70934,0.72023,0.50145,0.49419,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65815,SRR15626553,SRX11923620,SRS9937138,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 C2,GSM5538882,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,W2 C2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,GSM5538882,GSM5538882: W2 C2; Danio rerio; RNA Seq,GSM5538882,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538882,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_C2_1.fq.gz W2_C2_2.fq.gz,fastq fastq,9734471313.0,32968420.0,GSM5538882 r1,,A:2724735296;C:2009064775;G:2033048131;T:2966320646;N:1302465,,,,,2724735296,2009064775,2033048131,2966320646,1302465,SRX11923620,SRS9937138,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.7713,0.78947,0.11743,0.11671,0.71741,0.72736,0.49335,0.4863,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65816,SRR15626552,SRX11923619,SRS9937137,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 C1,GSM5538881,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,W2 C1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury,GSM5538881,GSM5538881: W2 C1; Danio rerio; RNA Seq,GSM5538881,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538881,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_C1_1.fq.gz W2_C1_2.fq.gz,fastq fastq,9082436552.0,30805602.0,GSM5538881 r1,,A:2559732121;C:1843621019;G:1872765497;T:2804939348;N:1378567,,,,,2559732121,1843621019,1872765497,2804939348,1378567,SRX11923619,SRS9937137,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.76943,0.78719,0.13099,0.13069,0.7259,0.73679,0.51491,0.39397,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65817,SRR15626551,SRX11923618,SRS9937136,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 R5,GSM5538880,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,W2 R5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,GSM5538880,GSM5538880: W2 R5; Danio rerio; RNA Seq,GSM5538880,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538880,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_R5_1.fq.gz W2_R5_2.fq.gz,fastq fastq,13733467500.0,45778225.0,GSM5538880 r1,0:150 1:150,A:3893031167;C:2866552637;G:2882457798;T:4090098547;N:1327351,150,150,,,3893031167,2866552637,2882457798,4090098547,1327351,SRX11923618,SRS9937136,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92215,0.91781,0.10294,0.10091,0.73434,0.74164,0.50738,0.50448,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65818,SRR15626550,SRX11923617,SRS9937135,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 R4,GSM5538879,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,W2 R4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,GSM5538879,GSM5538879: W2 R4; Danio rerio; RNA Seq,GSM5538879,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538879,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_R4_1.fq.gz W2_R4_2.fq.gz,fastq fastq,11955951600.0,39853172.0,GSM5538879 r1,0:150 1:150,A:3384460570;C:2474116532;G:2513217291;T:3582811941;N:1345266,150,150,,,3384460570,2474116532,2513217291,3582811941,1345266,SRX11923617,SRS9937135,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.9114,0.90987,0.09871,0.09717,0.73675,0.75148,0.50932,0.50986,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65819,SRR15626549,SRX11923616,SRS9937134,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 R3,GSM5538878,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,W2 R3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,GSM5538878,GSM5538878: W2 R3; Danio rerio; RNA Seq,GSM5538878,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538878,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_R3_1.fq.gz W2_R3_2.fq.gz,fastq fastq,11388586527.0,38223361.0,GSM5538878 r1,,A:3239034105;C:2424523990;G:2400765702;T:3319676527;N:4586203,,,,,3239034105,2424523990,2400765702,3319676527,4586203,SRX11923616,SRS9937134,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.93006,0.93152,0.13219,0.1324,0.71202,0.72316,0.46964,0.46882,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65820,SRR15626548,SRX11923615,SRS9937132,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 R2,GSM5538877,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,W2 R2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,GSM5538877,GSM5538877: W2 R2; Danio rerio; RNA Seq,GSM5538877,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538877,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_R2_1.fq.gz W2_R2_2.fq.gz,fastq fastq,10857439998.0,36629327.0,GSM5538877 r1,,A:3065308254;C:2244107418;G:2279781972;T:3267100338;N:1142016,,,,,3065308254,2244107418,2279781972,3267100338,1142016,SRX11923615,SRS9937132,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.81356,0.80696,0.11265,0.11068,0.72184,0.73456,0.48354,0.47728,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65821,SRR15626547,SRX11923614,SRS9937133,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W2 R1,GSM5538876,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,W2 R1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury,GSM5538876,GSM5538876: W2 R1; Danio rerio; RNA Seq,GSM5538876,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538876,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W2_R1_1.fq.gz W2_R1_2.fq.gz,fastq fastq,11341017399.0,38401504.0,GSM5538876 r1,,A:3207542121;C:2323545802;G:2348890309;T:3459431647;N:1607520,,,,,3207542121,2323545802,2348890309,3459431647,1607520,SRX11923614,SRS9937133,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.83184,0.84917,0.10758,0.10732,0.73699,0.7445,0.54011,0.53193,150,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65822,SRR15626546,SRX11923613,SRS9937131,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 C5,GSM5538875,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,W1 C5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,GSM5538875,GSM5538875: W1 C5; Danio rerio; RNA Seq,GSM5538875,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_C5_1.fq.gz W1_C5_2.fq.gz,fastq fastq,11249022600.0,37496742.0,GSM5538875 r1,0:150 1:150,A:3152341668;C:2390909295;G:2404570914;T:3300128090;N:1072633,150,150,,,3152341668,2390909295,2404570914,3300128090,1072633,SRX11923613,SRS9937131,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92641,0.92074,0.09283,0.09209,0.73105,0.7388,0.52978,0.514,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65823,SRR15626545,SRX11923612,SRS9937130,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 C4,GSM5538874,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,W1 C4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,GSM5538874,GSM5538874: W1 C4; Danio rerio; RNA Seq,GSM5538874,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538874,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_C4_1.fq.gz W1_C4_2.fq.gz,fastq fastq,12941095500.0,43136985.0,GSM5538874 r1,0:150 1:150,A:3634175324;C:2714886172;G:2737085820;T:3852831271;N:2116913,150,150,,,3634175324,2714886172,2737085820,3852831271,2116913,SRX11923612,SRS9937130,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.91641,0.91602,0.10958,0.10925,0.72955,0.73959,0.53161,0.51852,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65824,SRR15626544,SRX11923611,SRS9937129,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 C3,GSM5538873,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,W1 C3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,GSM5538873,GSM5538873: W1 C3; Danio rerio; RNA Seq,GSM5538873,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538873,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_C3_1.fq.gz W1_C3_2.fq.gz,fastq fastq,13936313921.0,46809823.0,GSM5538873 r1,,A:3961118753;C:2959742143;G:2931217720;T:4078708920;N:5526385,,,,,3961118753,2959742143,2931217720,4078708920,5526385,SRX11923611,SRS9937129,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92907,0.92635,0.13776,0.13693,0.71007,0.7219,0.50164,0.503,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65825,SRR15626543,SRX11923610,SRS9937128,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 C2,GSM5538872,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,W1 C2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,GSM5538872,GSM5538872: W1 C2; Danio rerio; RNA Seq,GSM5538872,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538872,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_C2_1.fq.gz W1_C2_2.fq.gz,fastq fastq,10863959491.0,36713522.0,GSM5538872 r1,,A:3045882932;C:2255239365;G:2294328860;T:3267345863;N:1162471,,,,,3045882932,2255239365,2294328860,3267345863,1162471,SRX11923610,SRS9937128,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.74749,0.74175,0.11328,0.11041,0.71701,0.72772,0.50737,0.50743,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65826,SRR15626542,SRX11923609,SRS9937127,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 C1,GSM5538871,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,W1 C1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury,GSM5538871,GSM5538871: W1 C1; Danio rerio; RNA Seq,GSM5538871,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_C1_1.fq.gz W1_C1_2.fq.gz,fastq fastq,9041395405.0,30629306.0,GSM5538871 r1,,A:2497325427;C:1907249915;G:1926778789;T:2708703938;N:1337336,,,,,2497325427,1907249915,1926778789,2708703938,1337336,SRX11923609,SRS9937127,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.84841,0.85222,0.12779,0.12199,0.7097,0.72372,0.52363,0.51259,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65827,SRR15626541,SRX11923608,SRS9937126,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 R5,GSM5538870,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,W1 R5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,GSM5538870,GSM5538870: W1 R5; Danio rerio; RNA Seq,GSM5538870,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_R5_1.fq.gz W1_R5_2.fq.gz,fastq fastq,12916604400.0,43055348.0,GSM5538870 r1,0:150 1:150,A:3648889898;C:2717488564;G:2731231996;T:3817740667;N:1253275,150,150,,,3648889898,2717488564,2731231996,3817740667,1253275,SRX11923608,SRS9937126,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92069,0.9168,0.08589,0.08501,0.73981,0.74582,0.5354,0.52462,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65828,SRR15626540,SRX11923607,SRS9937125,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 R4,GSM5538869,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,W1 R4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,GSM5538869,GSM5538869: W1 R4; Danio rerio; RNA Seq,GSM5538869,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_R4_1.fq.gz W1_R4_2.fq.gz,fastq fastq,11607402900.0,38691343.0,GSM5538869 r1,0:150 1:150,A:3285548269;C:2400691541;G:2419353169;T:3499826563;N:1983358,150,150,,,3285548269,2400691541,2419353169,3499826563,1983358,SRX11923607,SRS9937125,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.90628,0.90638,0.10284,0.10084,0.74119,0.7516,0.56967,0.55805,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65829,SRR15626539,SRX11923606,SRS9937124,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 R3,GSM5538868,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,W1 R3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,GSM5538868,GSM5538868: W1 R3; Danio rerio; RNA Seq,GSM5538868,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_R3_1.fq.gz W1_R3_2.fq.gz,fastq fastq,12284640305.0,41269517.0,GSM5538868 r1,,A:3508836269;C:2584576349;G:2559159651;T:3627220752;N:4847284,,,,,3508836269,2584576349,2559159651,3627220752,4847284,SRX11923606,SRS9937124,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92661,0.92684,0.16459,0.16558,0.70934,0.72285,0.51041,0.50635,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65830,SRR15626538,SRX11923605,SRS9937123,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 R2,GSM5538867,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,W1 R2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,GSM5538867,GSM5538867: W1 R2; Danio rerio; RNA Seq,GSM5538867,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_R2_1.fq.gz W1_R2_2.fq.gz,fastq fastq,9613189318.0,32414297.0,GSM5538867 r1,,A:2694360914;C:2005932920;G:2043314603;T:2868647636;N:933245,,,,,2694360914,2005932920,2043314603,2868647636,933245,SRX11923605,SRS9937123,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.76619,0.73756,0.12558,0.12014,0.71147,0.72839,0.49309,0.49039,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65831,SRR15626537,SRX11923604,SRS9937121,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,W1 R1,GSM5538866,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,W1 R1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury,GSM5538866,GSM5538866: W1 R1; Danio rerio; RNA Seq,GSM5538866,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,W1_R1_1.fq.gz W1_R1_2.fq.gz,fastq fastq,7386883792.0,38487420.0,GSM5538866 r1,,A:2066234577;C:1588682954;G:1585227765;T:2145801527;N:936969,,,,,2066234577,1588682954,1585227765,2145801527,936969,SRX11923604,SRS9937121,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.8001,0.79574,0.12188,0.11493,0.82319,0.83173,0.50624,0.50244,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65832,SRR15626536,SRX11923603,SRS9937122,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,C C5,GSM5538865,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,C C5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,GSM5538865,GSM5538865: C C5; Danio rerio; RNA Seq,GSM5538865,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,C_C5_1.fq.gz C_C5_2.fq.gz,fastq fastq,10481010900.0,34936703.0,GSM5538865 r1,0:150 1:150,A:3033441666;C:2163397542;G:2160648918;T:3122508289;N:1014485,150,150,,,3033441666,2163397542,2160648918,3122508289,1014485,SRX11923603,SRS9937122,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.92492,0.92322,0.09913,0.09708,0.75584,0.76278,0.41494,0.39986,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65833,SRR15626535,SRX11923602,SRS9937120,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,C C4,GSM5538864,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,C C4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,GSM5538864,GSM5538864: C C4; Danio rerio; RNA Seq,GSM5538864,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,C_C4_1.fq.gz C_C4_2.fq.gz,fastq fastq,13743878400.0,45812928.0,GSM5538864 r1,0:150 1:150,A:3950812518;C:2815585550;G:2826024540;T:4149189277;N:2266515,150,150,,,3950812518,2815585550,2826024540,4149189277,2266515,SRX11923602,SRS9937120,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.91264,0.90781,0.10415,0.10052,0.75623,0.76414,0.46029,0.44137,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65834,SRR15626534,SRX11923601,SRS9937119,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,C C3,GSM5538863,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,C C3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,GSM5538863,GSM5538863: C C3; Danio rerio; RNA Seq,GSM5538863,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,C_C3_1.fq.gz C_C3_2.fq.gz,fastq fastq,10004690274.0,33763075.0,GSM5538863 r1,,A:2912837817;C:2012257307;G:2009657924;T:3069767818;N:169408,,,,,2912837817,2012257307,2009657924,3069767818,169408,SRX11923601,SRS9937119,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.78488,0.77428,0.16138,0.15293,0.7346,0.75434,0.47034,0.45043,130,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65835,SRR15626533,SRX11923600,SRS9937118,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,C C2,GSM5538862,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,C C2,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,GSM5538862,GSM5538862: C C2; Danio rerio; RNA Seq,GSM5538862,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,C_C2_1.fq.gz C_C2_2.fq.gz,fastq fastq,12342833153.0,41656373.0,GSM5538862 r1,,A:3479483357;C:2557023755;G:2575718106;T:3729085258;N:1522677,,,,,3479483357,2557023755,2575718106,3729085258,1522677,SRX11923600,SRS9937118,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.81303,0.8134,0.10478,0.10146,0.74148,0.75239,0.44031,0.4289,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65836,SRR15626532,SRX11923599,SRS9937117,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,C C1,GSM5538861,,source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,C C1,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured,GSM5538861,GSM5538861: C C1; Danio rerio; RNA Seq,GSM5538861,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,C_C1_1.fq.gz C_C1_2.fq.gz,fastq fastq,10829115925.0,36675945.0,GSM5538861 r1,,A:3087677087;C:2185500105;G:2207404987;T:3346933841;N:1599905,,,,,3087677087,2185500105,2207404987,3346933841,1599905,SRX11923599,SRS9937117,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.86,0.86399,0.19457,0.18642,0.72616,0.74093,0.54866,0.52664,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65837,SRR15626531,SRX11923598,SRS9937116,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,C R5,GSM5538860,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured,C R5,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured,GSM5538860,GSM5538860: C R5; Danio rerio; RNA Seq,GSM5538860,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,C_R5_1.fq.gz C_R5_2.fq.gz,fastq fastq,13680284700.0,45600949.0,GSM5538860 r1,0:150 1:150,A:3941966047;C:2822961394;G:2831655507;T:4082375276;N:1326476,150,150,,,3941966047,2822961394,2831655507,4082375276,1326476,SRX11923598,SRS9937116,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.9179,0.91819,0.08491,0.08411,0.76114,0.76635,0.45434,0.44742,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65838,SRR15626530,SRX11923597,SRS9937115,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,C R4,GSM5538859,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured,C R4,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured,GSM5538859,GSM5538859: C R4; Danio rerio; RNA Seq,GSM5538859,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,C_R4_1.fq.gz C_R4_2.fq.gz,fastq fastq,13264501200.0,44215004.0,GSM5538859 r1,0:150 1:150,A:3823575952;C:2700864933;G:2712149070;T:4025644258;N:2266987,150,150,,,3823575952,2700864933,2712149070,4025644258,2266987,SRX11923597,SRS9937115,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.91094,0.90944,0.09845,0.09521,0.76708,0.77833,0.47031,0.43887,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System
65839,SRR15626529,SRX11923596,SRS9937114,SRP334272,PRJNA758088,Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury,GSE182868,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue  the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one  two  four  and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen  and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,C R3,GSM5538858,,source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured,C R3,Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing ploy N and low quality reads from raw data. At the same time  Q20  Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced  considers the effect of sequencing depth and gene length for the reads count at the same time  and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured,GSM5538858,GSM5538858: C R3; Danio rerio; RNA Seq,GSM5538858,,1,Spinal cord segments were isolated  flash frozen on dry ice  and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5538858,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334272,,loader:fastq load.py,C_R3_1.fq.gz C_R3_2.fq.gz,fastq fastq,9668631408.0,32685030.0,GSM5538858 r1,,A:2796307940;C:1932208926;G:1949362622;T:2989642567;N:1109353,,,,,2796307940,1932208926,1949362622,2989642567,1109353,SRX11923596,SRS9937114,SRA1284220,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.80284,0.80264,0.12886,0.12432,0.75004,0.76459,0.47533,0.47134,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2021-08-26,Undetermined,Adult,Spinal Cord,Nervous System