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
15028,ERR594449,ERX552402,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 010,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_010_R1.fastq.gz McGrail_PT_MM02_010_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 010 R,0:100 1:100,A:871527648;C:730105705;G:727172263;T:866698092;N:4496292,100,100,,,871527648,730105705,727172263,866698092,4496292,ERX552402,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92177,0.92501,0.1237,0.1262,0.69844,0.7009,0.49781,0.4982,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15029,ERR594457,ERX552401,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 002,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_002_R1.fastq.gz McGrail_PT_MM02_002_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 002 R,0:100 1:100,A:872387737;C:732112926;G:726274702;T:868026782;N:1197853,100,100,,,872387737,732112926,726274702,868026782,1197853,ERX552401,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92719,0.92684,0.126,0.12696,0.69684,0.70118,0.49645,0.50037,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15030,ERR594456,ERX552400,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 004,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_004_R2.fastq.gz McGrail_T_MM01_004_R1.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 004 R,0:100 1:100,A:849885320;C:752565271;G:741295555;T:853272249;N:2981605,100,100,,,849885320,752565271,741295555,853272249,2981605,ERX552400,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93431,0.93209,0.09121,0.09114,0.67842,0.68065,0.49543,0.48591,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15031,ERR594431,ERX552399,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 014,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_014_R1.fastq.gz MM03_WT_L003_014_R2.fastq.gz,fastq fastq,2051137800.0,10255689.0,E MTAB 2886:MM03 WT L003 014 R,0:100 1:100,A:574425675;C:454197762;G:448836898;T:573386204;N:291261,100,100,,,574425675,454197762,448836898,573386204,291261,ERX552399,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91659,0.91612,0.14679,0.14915,0.7163,0.72188,0.49275,0.49876,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15032,ERR594437,ERX552398,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 006,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_006_R1.fastq.gz MM03_WT_L003_006_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 006 R,0:100 1:100,A:892528148;C:712696530;G:702466589;T:891189817;N:1118916,100,100,,,892528148,712696530,702466589,891189817,1118916,ERX552398,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91798,0.9161,0.14538,0.14613,0.71401,0.71656,0.48443,0.48666,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15033,ERR594420,ERX552397,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 014,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_014_R1.fastq.gz McGrail_PT_MM02_014_R2.fastq.gz,fastq fastq,2883852800.0,14419264.0,E MTAB 2886:McGrail PT MM02 014 R,0:100 1:100,A:787372572;C:658074713;G:654251401;T:783994205;N:159909,100,100,,,787372572,658074713,654251401,783994205,159909,ERX552397,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92417,0.9255,0.12479,0.12619,0.69942,0.7035,0.50149,0.49379,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15034,ERR594450,ERX552396,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 014,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_014_R1.fastq.gz McGrail_T_MM01_014_R2.fastq.gz,fastq fastq,632445400.0,3162227.0,E MTAB 2886:McGrail T MM01 014 R,0:100 1:100,A:168708082;C:147923885;G:146292680;T:169438791;N:81962,100,100,,,168708082,147923885,146292680,169438791,81962,ERX552396,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93335,0.93318,0.09287,0.09485,0.68205,0.68846,0.4841,0.49015,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15035,ERR594453,ERX552395,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 011,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_011_R1.fastq.gz McGrail_T_MM01_011_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 011 R,0:100 1:100,A:852133250;C:751414688;G:741468348;T:854136333;N:847381,100,100,,,852133250,751414688,741468348,854136333,847381,ERX552395,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93354,0.93309,0.09259,0.09299,0.68085,0.68347,0.48686,0.48742,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15036,ERR594429,ERX552394,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 002,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_002_R1.fastq.gz McGrail_T_MM01_002_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 002 R,0:100 1:100,A:851061858;C:752624348;G:741241133;T:854588994;N:483667,100,100,,,851061858,752624348,741241133,854588994,483667,ERX552394,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.9341,0.93285,0.09214,0.09303,0.68036,0.68465,0.4888,0.4918,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15037,ERR594444,ERX552393,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 007,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_007_R1.fastq.gz McGrail_PT_MM02_007_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 007 R,0:100 1:100,A:871235248;C:733455837;G:726280934;T:868628388;N:399593,100,100,,,871235248,733455837,726280934,868628388,399593,ERX552393,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92587,0.9237,0.12434,0.12596,0.69729,0.70473,0.49751,0.49568,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15038,ERR594436,ERX552392,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 010,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_010_R1.fastq.gz MM03_WT_L003_010_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 010 R,0:100 1:100,A:893317570;C:712391457;G:703064824;T:890653459;N:572690,100,100,,,893317570,712391457,703064824,890653459,572690,ERX552392,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91775,0.91713,0.14296,0.14486,0.7136,0.71638,0.50074,0.49246,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15039,ERR594454,ERX552391,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 003,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_003_R1.fastq.gz MM03_WT_L003_003_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 003 R,0:100 1:100,A:891513936;C:713529681;G:702140879;T:891351829;N:1463675,100,100,,,891513936,713529681,702140879,891351829,1463675,ERX552391,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91714,0.91621,0.14364,0.14479,0.71384,0.71967,0.48172,0.4892,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15040,ERR594422,ERX552378,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 001,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_001_R1.fastq.gz McGrail_T_MM01_001_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 001 R,0:100 1:100,A:849397709;C:754334352;G:741772141;T:853832972;N:662826,100,100,,,849397709,754334352,741772141,853832972,662826,ERX552378,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93478,0.93297,0.09219,0.09261,0.67949,0.68205,0.48892,0.47759,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15041,ERR594433,ERX552377,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 009,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_009_R1.fastq.gz MM03_WT_L003_009_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 009 R,0:100 1:100,A:895908752;C:709459693;G:701325342;T:892915017;N:391196,100,100,,,895908752,709459693,701325342,892915017,391196,ERX552377,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91776,0.91744,0.14402,0.14626,0.71435,0.71794,0.48624,0.49768,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15042,ERR594419,ERX552376,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 011,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_011_R1.fastq.gz MM03_WT_L003_011_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 011 R,0:100 1:100,A:894536120;C:711072714;G:702055612;T:891872676;N:462878,100,100,,,894536120,711072714,702055612,891872676,462878,ERX552376,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91628,0.91598,0.14427,0.14587,0.71293,0.71575,0.48688,0.49317,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15043,ERR594447,ERX552375,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 004,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_004_R1.fastq.gz MM03_WT_L003_004_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 004 R,0:100 1:100,A:893087129;C:711953975;G:702111417;T:891168240;N:1679239,100,100,,,893087129,711953975,702111417,891168240,1679239,ERX552375,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91793,0.91708,0.14418,0.1457,0.71052,0.71405,0.50617,0.49339,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15044,ERR594441,ERX552374,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 004,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_004_R1.fastq.gz McGrail_PT_MM02_004_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 004 R,0:100 1:100,A:869694755;C:734631291;G:727458512;T:866857422;N:1358020,100,100,,,869694755,734631291,727458512,866857422,1358020,ERX552374,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92607,0.9248,0.12414,0.12446,0.69686,0.6995,0.50202,0.50333,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15045,ERR594455,ERX552373,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 002,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_002_R1.fastq.gz MM03_WT_L003_002_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 002 R,0:100 1:100,A:894222634;C:711188537;G:702167816;T:891816353;N:604660,100,100,,,894222634,711188537,702167816,891816353,604660,ERX552373,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.9174,0.91577,0.14516,0.14534,0.71342,0.71756,0.48084,0.50033,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15046,ERR594439,ERX552410,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 007,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_007_R1.fastq.gz McGrail_T_MM01_007_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 007 R,0:100 1:100,A:850777874;C:752786693;G:741650641;T:854268527;N:516265,100,100,,,850777874,752786693,741650641,854268527,516265,ERX552410,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93398,0.93264,0.0917,0.09232,0.67878,0.68172,0.48311,0.48417,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15047,ERR594426,ERX552409,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 012,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_012_R1.fastq.gz McGrail_T_MM01_012_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 012 R,0:100 1:100,A:851190790;C:752415289;G:742719596;T:852979263;N:695062,100,100,,,851190790,752415289,742719596,852979263,695062,ERX552409,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93297,0.9327,0.09093,0.09105,0.68043,0.68282,0.48563,0.48327,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15048,ERR594417,ERX552390,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 007,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_007_R1.fastq.gz MM03_WT_L003_007_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 007 R,0:100 1:100,A:893566548;C:711756657;G:701577232;T:892509486;N:590077,100,100,,,893566548,711756657,701577232,892509486,590077,ERX552390,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.9176,0.91644,0.14542,0.14641,0.71358,0.71713,0.48742,0.50207,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15049,ERR594418,ERX552389,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 008,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_008_R1.fastq.gz McGrail_T_MM01_008_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 008 R,0:100 1:100,A:851314323;C:752411525;G:742349039;T:853577153;N:347960,100,100,,,851314323,752411525,742349039,853577153,347960,ERX552389,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93343,0.93187,0.09175,0.09249,0.68016,0.68164,0.47952,0.48824,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15050,ERR594440,ERX552388,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 013,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_013_R1.fastq.gz McGrail_T_MM01_013_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 013 R,0:100 1:100,A:852425880;C:750595968;G:742140159;T:854286637;N:551356,100,100,,,852425880,750595968,742140159,854286637,551356,ERX552388,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93231,0.93338,0.09134,0.09313,0.67945,0.68256,0.48693,0.48084,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15051,ERR594430,ERX552387,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 006,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_006_R1.fastq.gz McGrail_PT_MM02_006_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 006 R,0:100 1:100,A:869575312;C:734964855;G:727824124;T:866586174;N:1049535,100,100,,,869575312,734964855,727824124,866586174,1049535,ERX552387,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.9265,0.92348,0.12368,0.12345,0.69818,0.70017,0.4966,0.50082,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15052,ERR594445,ERX552386,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 012,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_012_R1.fastq.gz McGrail_PT_MM02_012_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 012 R,0:100 1:100,A:870939166;C:729921300;G:724359208;T:865762186;N:9018140,100,100,,,870939166,729921300,724359208,865762186,9018140,ERX552386,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92143,0.92467,0.1229,0.12533,0.69828,0.70015,0.50049,0.4981,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15053,ERR594434,ERX552385,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 013,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_013_R1.fastq.gz MM03_WT_L003_013_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 013 R,0:100 1:100,A:894614606;C:711109946;G:702301073;T:891485450;N:488925,100,100,,,894614606,711109946,702301073,891485450,488925,ERX552385,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91697,0.91671,0.1447,0.14584,0.71327,0.7176,0.48116,0.49462,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15054,ERR594443,ERX552372,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 011,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_011_R1.fastq.gz McGrail_PT_MM02_011_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 011 R,0:100 1:100,A:869080240;C:728959737;G:723451216;T:862492567;N:16016240,100,100,,,869080240,728959737,723451216,862492567,16016240,ERX552372,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.91732,0.92471,0.12164,0.12427,0.69739,0.69773,0.50246,0.50104,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15055,ERR594425,ERX552371,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 003,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_003_R1.fastq.gz McGrail_T_MM01_003_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 003 R,0:100 1:100,A:849037687;C:754289116;G:741157518;T:854195808;N:1319871,100,100,,,849037687,754289116,741157518,854195808,1319871,ERX552371,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93418,0.93244,0.09187,0.09177,0.67919,0.68278,0.49475,0.4843,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15056,ERR594442,ERX552370,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 013,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_013_R1.fastq.gz McGrail_PT_MM02_013_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 013 R,0:100 1:100,A:871688870;C:733183478;G:727799783;T:867055926;N:271943,100,100,,,871688870,733183478,727799783,867055926,271943,ERX552370,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92516,0.92506,0.12387,0.12596,0.69601,0.69852,0.49866,0.50071,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15057,ERR594438,ERX552369,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 005,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_005_R1.fastq.gz McGrail_T_MM01_005_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 005 R,0:100 1:100,A:849484270;C:753864282;G:741293874;T:854126120;N:1231454,100,100,,,849484270,753864282,741293874,854126120,1231454,ERX552369,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93385,0.93181,0.09285,0.0935,0.67882,0.68209,0.48445,0.49581,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15058,ERR594452,ERX552408,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 001,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_001_R1.fastq.gz McGrail_PT_MM02_001_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 001 R,0:100 1:100,A:869685021;C:734763957;G:726895796;T:867397539;N:1257687,100,100,,,869685021,734763957,726895796,867397539,1257687,ERX552408,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92687,0.92533,0.12345,0.12461,0.69749,0.70055,0.49809,0.49848,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15059,ERR594446,ERX552407,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 006,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_006_R1.fastq.gz McGrail_T_MM01_006_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 006 R,0:100 1:100,A:850456499;C:753116092;G:742193025;T:853616872;N:617512,100,100,,,850456499,753116092,742193025,853616872,617512,ERX552407,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.9331,0.93179,0.09172,0.09219,0.67917,0.68158,0.48168,0.48339,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15060,ERR594428,ERX552406,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 008,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_008_R1.fastq.gz McGrail_PT_MM02_008_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 008 R,0:100 1:100,A:871557679;C:733260378;G:727404860;T:867366205;N:410878,100,100,,,871557679,733260378,727404860,867366205,410878,ERX552406,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92806,0.92602,0.12481,0.12546,0.69771,0.70086,0.50152,0.50006,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15061,ERR594423,ERX552405,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 008,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_008_R1.fastq.gz MM03_WT_L003_008_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 008 R,0:100 1:100,A:894053419;C:711591129;G:702881160;T:891029747;N:444545,100,100,,,894053419,711591129,702881160,891029747,444545,ERX552405,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91542,0.91567,0.14469,0.14612,0.71289,0.7161,0.49104,0.48972,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15062,ERR594424,ERX552404,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 005,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_005_R1.fastq.gz MM03_WT_L003_005_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 005 R,0:100 1:100,A:892331319;C:712533931;G:701570336;T:891914366;N:1650048,100,100,,,892331319,712533931,701570336,891914366,1650048,ERX552404,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91746,0.91624,0.14471,0.14581,0.71498,0.71985,0.48939,0.49411,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15063,ERR594416,ERX552403,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 005,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_005_R1.fastq.gz McGrail_PT_MM02_005_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 005 R,0:100 1:100,A:870557258;C:733600250;G:726156781;T:868210376;N:1475335,100,100,,,870557258,733600250,726156781,868210376,1475335,ERX552403,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92621,0.92323,0.12426,0.1247,0.69836,0.70418,0.50259,0.49996,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15064,ERR594427,ERX552384,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 009,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_009_R1.fastq.gz McGrail_PT_MM02_009_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 009 R,0:100 1:100,A:872849771;C:731277001;G:727186355;T:868245858;N:441015,100,100,,,872849771,731277001,727186355,868245858,441015,ERX552384,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92396,0.92581,0.12417,0.12625,0.69879,0.70189,0.50046,0.50188,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15065,ERR594432,ERX552383,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 010,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_010_R1.fastq.gz McGrail_T_MM01_010_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 010 R,0:100 1:100,A:850551531;C:753023540;G:742554950;T:852763762;N:1106217,100,100,,,850551531,753023540,742554950,852763762,1106217,ERX552383,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93373,0.93132,0.09087,0.09072,0.67898,0.68083,0.49414,0.48713,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15066,ERR594435,ERX552382,ERS539974,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM01 T,SAMEA2747166,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail T MM01 009,MM01 T,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_T_MM01_009_R1.fastq.gz McGrail_T_MM01_009_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail T MM01 009 R,0:100 1:100,A:852308329;C:751198229;G:741341036;T:854788512;N:363894,100,100,,,852308329,751198229,741341036,854788512,363894,ERX552382,ERS539974,ERA356220,Iowa State University,Iowa State University,2,0.93348,0.93139,0.09329,0.09409,0.68071,0.68359,0.48469,0.49176,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15067,ERR594421,ERX552381,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 012,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_012_R1.fastq.gz MM03_WT_L003_012_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 012 R,0:100 1:100,A:894330816;C:710946707;G:702107786;T:892049601;N:565090,100,100,,,894330816,710946707,702107786,892049601,565090,ERX552381,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91723,0.91629,0.14541,0.14611,0.71427,0.71719,0.49682,0.49865,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15068,ERR594451,ERX552380,ERS539976,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM03 WT,SAMEA2747168,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:MM03 WT L003 001,MM03 WT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,MM03_WT_L003_001_R1.fastq.gz MM03_WT_L003_001_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:MM03 WT L003 001 R,0:100 1:100,A:892492791;C:713070365;G:702444959;T:891434993;N:556892,100,100,,,892492791,713070365,702444959,891434993,556892,ERX552380,ERS539976,ERA356220,Iowa State University,Iowa State University,2,0.91795,0.91727,0.14627,0.14672,0.71382,0.71636,0.48819,0.49971,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
15069,ERR594448,ERX552379,ERS539975,ERP006866,PRJEB7172,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E-MTAB-2886,Transcriptome Analysis,Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.,,,Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,MM02 PT,SAMEA2747167,Iowa State University,ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,E MTAB 2886:McGrail PT MM02 003,MM02 PT,Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  “Wild Type”  contained three pooled retinas from 6 mpf wild type adults. The second sample  “Pretumor”  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  “Tumor”  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.,Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP006866,Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line,ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16,McGrail_PT_MM02_003_R1.fastq.gz McGrail_PT_MM02_003_R2.fastq.gz,fastq fastq,3200000000.0,16000000.0,E MTAB 2886:McGrail PT MM02 003 R,0:100 1:100,A:870188856;C:734020429;G:726554216;T:867996712;N:1239787,100,100,,,870188856,734020429,726554216,867996712,1239787,ERX552379,ERS539975,ERA356220,Iowa State University,Iowa State University,2,0.92516,0.92471,0.12313,0.12411,0.69686,0.69982,0.49257,0.49644,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2014-12-11,Adult,Adult,Multi-tissue,Multi-system
24582,SRR25462250,SRX21195051,SRS18453977,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 3,GSM7669027,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669027,GSM7669027: PG HE 8mpf 3; Danio rerio; RNA Seq,GSM7669027 r1,GSM7669027,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_3_S11_L003_R1_001.fastq.gz HE_PG_8mpf_3_S11_L003_R2_001.fastq.gz,fastq fastq,7161373434.0,60309247.0,GSM7669027 r1,0:59.39 1:59.35,A:1783731260;C:1744025029;G:1733970346;T:1880173306;N:19473493,59,59,,,1783731260,1744025029,1733970346,1880173306,19473493,SRX21195051,SRS18453977,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94187,0.94592,0.01475,0.01464,0.77447,0.77498,0.45855,0.4635,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24583,SRR25462251,SRX21195050,SRS18453976,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 2,GSM7669026,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669026,GSM7669026: PG HE 8mpf 2; Danio rerio; RNA Seq,GSM7669026 r1,GSM7669026,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_2_S7_L003_R1_001.fastq.gz HE_PG_8mpf_2_S7_L003_R2_001.fastq.gz,fastq fastq,3176994053.0,26828357.0,GSM7669026 r1,0:59.22 1:59.20,A:793619267;C:767135191;G:764404567;T:830643823;N:21191205,59,59,,,793619267,767135191,764404567,830643823,21191205,SRX21195050,SRS18453976,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93822,0.94226,0.01596,0.0161,0.77684,0.77772,0.47008,0.46904,59,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24584,SRR25462252,SRX21195049,SRS18453975,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 1,GSM7669025,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669025,GSM7669025: PG HE 8mpf 1; Danio rerio; RNA Seq,GSM7669025 r1,GSM7669025,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_1_S6_L003_R1_001.fastq.gz HE_PG_8mpf_1_S6_L003_R2_001.fastq.gz,fastq fastq,4587580737.0,38590260.0,GSM7669025 r1,0:59.45 1:59.43,A:1149031944;C:1121086335;G:1106925902;T:1203970839;N:6565717,59,59,,,1149031944,1121086335,1106925902,1203970839,6565717,SRX21195049,SRS18453975,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94032,0.9437,0.01481,0.01462,0.77682,0.77774,0.45843,0.4699,58,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24585,SRR25462253,SRX21195048,SRS18453974,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 3,GSM7669024,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669024,GSM7669024: PG WT 8mpf 3; Danio rerio; RNA Seq,GSM7669024 r1,GSM7669024,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_3_S8_L003_R2_001.fastq.gz WT_PG_8mpf_3_S8_L003_R1_001.fastq.gz,fastq fastq,3920821867.0,33089226.0,GSM7669024 r1,0:59.26 1:59.23,A:977738236;C:951999354;G:944769809;T:1023828622;N:22485846,59,59,,,977738236,951999354,944769809,1023828622,22485846,SRX21195048,SRS18453974,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94193,0.94555,0.01657,0.01646,0.76784,0.76919,0.47238,0.47016,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24586,SRR25462254,SRX21195047,SRS18453973,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 2,GSM7669023,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669023,GSM7669023: PG WT 8mpf 2; Danio rerio; RNA Seq,GSM7669023 r1,GSM7669023,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_2_S10_L003_R2_001.fastq.gz WT_PG_8mpf_2_S10_L003_R1_001.fastq.gz,fastq fastq,4917868553.0,41430484.0,GSM7669023 r1,0:59.37 1:59.33,A:1231173294;C:1195692797;G:1182545852;T:1292018757;N:16437853,59,59,,,1231173294,1195692797,1182545852,1292018757,16437853,SRX21195047,SRS18453973,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94048,0.94432,0.0178,0.0178,0.75645,0.7569,0.46332,0.46812,59,57,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24587,SRR25462255,SRX21195046,SRS18453972,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 1,GSM7669022,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669022,GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq,GSM7669022 r1,GSM7669022,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz,fastq fastq,3375380667.0,28408784.0,GSM7669022 r1,0:59.42 1:59.40,A:842316103;C:825987175;G:818715765;T:881225528;N:7136096,59,59,,,842316103,825987175,818715765,881225528,7136096,SRX21195046,SRS18453972,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94039,0.9444,0.0162,0.01617,0.7697,0.76986,0.47132,0.46938,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24588,SRR25462256,SRX21195045,SRS18453971,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 3,GSM7669021,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669021,GSM7669021: PG HE 50dpf 3; Danio rerio; RNA Seq,GSM7669021 r1,GSM7669021,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_3_S26_L003_R1_001.fastq.gz PG_HE_3_S26_L003_R2_001.fastq.gz,fastq fastq,4520051001.0,22984712.0,GSM7669021 r1,0:98.32 1:98.33,A:1134815259;C:1102592573;G:1104475707;T:1160918938;N:17248524,98,98,,,1134815259,1102592573,1104475707,1160918938,17248524,SRX21195045,SRS18453971,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93438,0.93937,0.01237,0.01252,0.78208,0.78192,0.48454,0.49474,99,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24589,SRR25462257,SRX21195044,SRS18453970,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 2,GSM7669020,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669020,GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq,GSM7669020 r1,GSM7669020,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz,fastq fastq,3915471868.0,19847479.0,GSM7669020 r1,0:98.64 1:98.64,A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274,98,98,,,982714666,957212118,961590362,1003408448,10546274,SRX21195044,SRS18453970,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93184,0.93552,0.01275,0.01275,0.78356,0.7835,0.49472,0.48841,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24590,SRR25462258,SRX21195043,SRS18453969,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 1,GSM7669019,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669019,GSM7669019: PG HE 50dpf 1; Danio rerio; RNA Seq,GSM7669019 r1,GSM7669019,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_1_S24_L003_R1_001.fastq.gz PG_HE_1_S24_L003_R2_001.fastq.gz,fastq fastq,4764998144.0,24264412.0,GSM7669019 r1,0:98.18 1:98.20,A:1194676445;C:1161648051;G:1165061360;T:1221860864;N:21751424,98,98,,,1194676445,1161648051,1165061360,1221860864,21751424,SRX21195043,SRS18453969,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.91864,0.92247,0.01213,0.01245,0.7949,0.79584,0.50422,0.50318,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24591,SRR25462259,SRX21195042,SRS18453968,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 3,GSM7669018,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669018,GSM7669018: PG WT 50dpf 3; Danio rerio; RNA Seq,GSM7669018 r1,GSM7669018,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_3_S23_L003_R1_001.fastq.gz PG_WT_3_S23_L003_R2_001.fastq.gz,fastq fastq,6204452412.0,31480139.0,GSM7669018 r1,0:98.55 1:98.54,A:1567898375;C:1505755791;G:1512895523;T:1599284546;N:18618177,98,98,,,1567898375,1505755791,1512895523,1599284546,18618177,SRX21195042,SRS18453968,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.9312,0.93599,0.01692,0.01686,0.76426,0.76439,0.46519,0.47751,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24592,SRR25462260,SRX21195041,SRS18453967,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 2,GSM7669017,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669017,GSM7669017: PG WT 50dpf 2; Danio rerio; RNA Seq,GSM7669017 r1,GSM7669017,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_2_S22_L003_R1_001.fastq.gz PG_WT_2_S22_L003_R2_001.fastq.gz,fastq fastq,3907759829.0,19906505.0,GSM7669017 r1,0:98.15 1:98.15,A:991973983;C:940499355;G:946342572;T:1011476708;N:17467211,98,98,,,991973983,940499355,946342572,1011476708,17467211,SRX21195041,SRS18453967,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.91435,0.9186,0.02035,0.02032,0.764,0.76321,0.48743,0.48644,97,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24593,SRR25462261,SRX21195040,SRS18453966,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 1,GSM7669016,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669016,GSM7669016: PG WT 50dpf 1; Danio rerio; RNA Seq,GSM7669016 r1,GSM7669016,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_1_S21_L003_R2_001.fastq.gz PG_WT_1_S21_L003_R1_001.fastq.gz,fastq fastq,7395136401.0,37752582.0,GSM7669016 r1,0:97.94 1:97.94,A:1865709287;C:1789949400;G:1796311820;T:1908470411;N:34695483,97,97,,,1865709287,1789949400,1796311820,1908470411,34695483,SRX21195040,SRS18453966,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.9216,0.92737,0.01817,0.01802,0.76601,0.76593,0.48894,0.4975,100,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24594,SRR25462243,SRX21195038,SRS18453964,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV  M3,GSM7669033,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV  M3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669033,GSM7669033: PV  M3; Danio rerio; RNA Seq,GSM7669033 r1,GSM7669033,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz,fastq fastq,4644457090.0,23465750.0,GSM7669033 r1,0:98.98 1:98.94,A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277,98,98,,,1196567358,1114203322,1109379777,1223156356,1150277,SRX21195038,SRS18453964,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94849,0.95248,0.02727,0.02708,0.73602,0.73718,0.48396,0.4855,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24595,SRR25462244,SRX21195037,SRS18453963,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV  M2,GSM7669032,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV  M2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669032,GSM7669032: PV  M2; Danio rerio; RNA Seq,GSM7669032 r1,GSM7669032,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz,fastq fastq,2464506276.0,12449948.0,GSM7669032 r1,0:98.99 1:98.96,A:632587002;C:593372099;G:591579950;T:646214108;N:753117,98,98,,,632587002,593372099,591579950,646214108,753117,SRX21195037,SRS18453963,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94889,0.9522,0.02585,0.02585,0.73669,0.73841,0.48398,0.48486,100,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24596,SRR25462245,SRX21195036,SRS18453962,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV  M1,GSM7669031,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing,PV  M1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ,GSM7669031,GSM7669031: PV  M1; Danio rerio; RNA Seq,GSM7669031 r1,GSM7669031,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz,fastq fastq,3634173229.0,18461903.0,GSM7669031 r1,0:98.44 1:98.41,A:930322973;C:875929476;G:875710056;T:948595199;N:3615525,98,98,,,930322973,875929476,875710056,948595199,3615525,SRX21195036,SRS18453962,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94787,0.95134,0.02457,0.02445,0.73762,0.73843,0.48244,0.48069,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24597,SRR25462246,SRX21195035,SRS18453961,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV  WT3,GSM7669030,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV  WT3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669030,GSM7669030: PV  WT3; Danio rerio; RNA Seq,GSM7669030 r1,GSM7669030,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT3_R2.fastq PV_WT3_R1.fastq,fastq fastq,2965772270.0,14976621.0,GSM7669030 r1,0:99.03 1:98.99,A:759343389;C:716154246;G:713466520;T:775995980;N:812135,99,98,,,759343389,716154246,713466520,775995980,812135,SRX21195035,SRS18453961,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.95027,0.95485,0.02356,0.02292,0.74422,0.74554,0.47974,0.48267,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24598,SRR25462247,SRX21195034,SRS18453960,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV  WT2,GSM7669029,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV  WT2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669029,GSM7669029: PV  WT2; Danio rerio; RNA Seq,GSM7669029 r1,GSM7669029,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT2_R2.fastq PV_WT2_R1.fastq,fastq fastq,2021387268.0,10195384.0,GSM7669029 r1,0:99.15 1:99.12,A:517788644;C:487363563;G:485168383;T:530550229;N:516449,99,99,,,517788644,487363563,485168383,530550229,516449,SRX21195034,SRS18453960,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.95113,0.9544,0.02394,0.02364,0.74168,0.74363,0.47881,0.47499,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24599,SRR25462248,SRX21195033,SRS18453959,SRP452269,PRJNA1000446,Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish,GSE239623,Transcriptome Analysis,Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study  we created an ybx1 mutant with CRISPR/Cas9  and showed that the folliculogenesis in the mutant ovary ybx1 /  was blocked at pre vitellogenic PV to early vitellogenic EV transition  leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 /  and the control ybx1+/  including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/   however  follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly  partial loss of p21 in heterozygous cdkn1a+/  could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/  females with normal follicle activation  in contrast to the PV EV blockade in ybx1 /  mutant. Interestingly  the follicle cells from the ybx1 /  mutant follicles displayed a poor proliferative activity in vitro; however  the cells from the ybx1 / p21+/  follicles resumed normal proliferation compared to that from the wildtype fish. In summary  we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a  a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade  we further isolated PV follicles from both WT ybx1+/+ and  ybx1 /  zebrafish. post RNA isolation  we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PV  WT1,GSM7669028,,source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing,PV  WT1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+,GSM7669028,GSM7669028: PV  WT1; Danio rerio; RNA Seq,GSM7669028 r1,GSM7669028,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452269,,,PV_WT1_R1.fastq PV_WT1_R2.fastq,fastq fastq,3244660111.0,16481925.0,GSM7669028 r1,0:98.44 1:98.42,A:831426044;C:781489498;G:779991004;T:848549246;N:3204319,98,98,,,831426044,781489498,779991004,848549246,3204319,SRX21195033,SRS18453959,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94779,0.95185,0.02328,0.02298,0.74294,0.74391,0.48052,0.47966,95,95,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Undetermined,Embryo,Gonad,Reproductive System
24652,SRR25487068,SRX21218619,SRS18475798,SRP452670,PRJNA1000968,CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo,GSE239788,Transcriptome Analysis,Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and  when mutated   leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice  the detailed impact of the  constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated.  We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired  skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably  in contrast to nexn  morphants  CRISPR/Cas9 nexn /  knockout embryos showed a milder phenotype without xxx development of a pronounced  pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest  some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced  and may mediate a sarcomere stabilizing function in nexn /  knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce  we generated a CRISPR/Cas9 mediated nexn  knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.,,pubmed:38114601,,nexn /   biological replicate 2,GSM7673294,,source name:whole organism|tissue:whole organism|genotype:nexn knockout|geo loc name:missing|collection date:missing,nexn /   biological replicate 2,Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics  INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference  run through Sentieon framework  along with the known gene models. eurofins genomics  INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics  INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise  gene wise read counts  TPM value and FPKM value,whole organism,,RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome  done by eurofins Genomics,,tissue:whole organism|genotype:nexn knockout,GSM7673294,GSM7673294: nexn /   biological replicate 2; Danio rerio; RNA Seq,GSM7673294 r1,GSM7673294,1,RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome  done by eurofins Genomics,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452670,,loader:fastq load.py,NG-33220_nexn_E2_mut3_lib700540_10254_1_2.fastq.gz NG-33220_nexn_E2_mut3_lib700540_10254_1_1.fastq.gz,fastq fastq,12821226686.0,42454393.0,GSM7673294 r1,0:151 1:151,A:3460123169;C:2958819646;G:3023309404;T:3378893399;N:81068,151,151,,,3460123169,2958819646,3023309404,3378893399,81068,SRX21218619,SRS18475798,SRA1684694,"Molecular Cardiology, Internal Medicine II, Uniklinik Ulm","Molecular Cardiology, Internal Medicine II, Uniklinik Ulm",2,0.96544,0.96684,0.07136,0.06827,0.66969,0.66914,0.44957,0.45604,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,bulk,bulk,,Germany,2023-08-01,Undetermined,Embryo,Whole Organism,All anatomical structures
24653,SRR25487069,SRX21218618,SRS18475797,SRP452670,PRJNA1000968,CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo,GSE239788,Transcriptome Analysis,Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and  when mutated   leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice  the detailed impact of the  constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated.  We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired  skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably  in contrast to nexn  morphants  CRISPR/Cas9 nexn /  knockout embryos showed a milder phenotype without xxx development of a pronounced  pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest  some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced  and may mediate a sarcomere stabilizing function in nexn /  knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce  we generated a CRISPR/Cas9 mediated nexn  knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.,,pubmed:38114601,,nexn /   biological replicate 1,GSM7673293,,source name:whole organism|tissue:whole organism|genotype:nexn knockout|geo loc name:missing|collection date:missing,nexn /   biological replicate 1,Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics  INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference  run through Sentieon framework  along with the known gene models. eurofins genomics  INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics  INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise  gene wise read counts  TPM value and FPKM value,whole organism,,RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome  done by eurofins Genomics,,tissue:whole organism|genotype:nexn knockout,GSM7673293,GSM7673293: nexn /   biological replicate 1; Danio rerio; RNA Seq,GSM7673293 r1,GSM7673293,1,RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome  done by eurofins Genomics,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452670,,loader:fastq load.py,NG-33220_nexn_E2_mut1_lib691942_10222_3_2.fastq.gz NG-33220_nexn_E2_mut1_lib691942_10222_3_1.fastq.gz,fastq fastq,6518650974.0,21584937.0,GSM7673293 r1,0:151 1:151,A:1776227735;C:1486881610;G:1503672330;T:1751641678;N:227621,151,151,,,1776227735,1486881610,1503672330,1751641678,227621,SRX21218618,SRS18475797,SRA1684694,"Molecular Cardiology, Internal Medicine II, Uniklinik Ulm","Molecular Cardiology, Internal Medicine II, Uniklinik Ulm",2,0.9619,0.96365,0.08223,0.07902,0.66967,0.66811,0.44763,0.45022,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,bulk,bulk,,Germany,2023-08-01,Undetermined,Embryo,Whole Organism,All anatomical structures
24654,SRR25487070,SRX21218617,SRS18475796,SRP452670,PRJNA1000968,CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo,GSE239788,Transcriptome Analysis,Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and  when mutated   leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice  the detailed impact of the  constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated.  We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired  skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably  in contrast to nexn  morphants  CRISPR/Cas9 nexn /  knockout embryos showed a milder phenotype without xxx development of a pronounced  pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest  some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced  and may mediate a sarcomere stabilizing function in nexn /  knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce  we generated a CRISPR/Cas9 mediated nexn  knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.,,pubmed:38114601,,nexn+/+  biological replicate 2,GSM7673292,,source name:whole organism|tissue:whole organism|genotype:WT|geo loc name:missing|collection date:missing,nexn+/+  biological replicate 2,Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics  INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference  run through Sentieon framework  along with the known gene models. eurofins genomics  INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics  INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise  gene wise read counts  TPM value and FPKM value,whole organism,,RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome  done by eurofins Genomics,,tissue:whole organism|genotype:WT,GSM7673292,GSM7673292: nexn+/+  biological replicate 2; Danio rerio; RNA Seq,GSM7673292 r1,GSM7673292,1,RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome  done by eurofins Genomics,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452670,,loader:fastq load.py,NG-33220_nexn_E2_sib3_lib693760_10227_1_1.fastq.gz NG-33220_nexn_E2_sib3_lib693760_10227_1_2.fastq.gz,fastq fastq,9966559304.0,33001852.0,GSM7673292 r1,0:151 1:151,A:2799666848;C:2201108797;G:2237142072;T:2728542087;N:99500,151,151,,,2799666848,2201108797,2237142072,2728542087,99500,SRX21218617,SRS18475796,SRA1684694,"Molecular Cardiology, Internal Medicine II, Uniklinik Ulm","Molecular Cardiology, Internal Medicine II, Uniklinik Ulm",2,0.95433,0.9562,0.11378,0.10948,0.68426,0.68302,0.45622,0.46107,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,bulk,bulk,,Germany,2023-08-01,Undetermined,Embryo,Whole Organism,All anatomical structures
24655,SRR25487071,SRX21218616,SRS18475795,SRP452670,PRJNA1000968,CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo,GSE239788,Transcriptome Analysis,Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and  when mutated   leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice  the detailed impact of the  constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated.  We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired  skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably  in contrast to nexn  morphants  CRISPR/Cas9 nexn /  knockout embryos showed a milder phenotype without xxx development of a pronounced  pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest  some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced  and may mediate a sarcomere stabilizing function in nexn /  knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce  we generated a CRISPR/Cas9 mediated nexn  knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq.,,pubmed:38114601,,nexn+/+  biological replicate 1,GSM7673291,,source name:whole organism|tissue:whole organism|genotype:WT|geo loc name:missing|collection date:missing,nexn+/+  biological replicate 1,Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics  INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference  run through Sentieon framework  along with the known gene models. eurofins genomics  INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics  INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise  gene wise read counts  TPM value and FPKM value,whole organism,,RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome  done by eurofins Genomics,,tissue:whole organism|genotype:WT,GSM7673291,GSM7673291: nexn+/+  biological replicate 1; Danio rerio; RNA Seq,GSM7673291 r1,GSM7673291,1,RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome  done by eurofins Genomics,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452670,,loader:fastq load.py,NG-33220_nexn_E2_sib2_lib693759_10227_2_1.fastq.gz NG-33220_nexn_E2_sib2_lib693759_10227_2_2.fastq.gz,fastq fastq,13610380470.0,45067485.0,GSM7673291 r1,0:151 1:151,A:3776423931;C:3037607848;G:3100752195;T:3694688167;N:908329,151,151,,,3776423931,3037607848,3100752195,3694688167,908329,SRX21218616,SRS18475795,SRA1684694,"Molecular Cardiology, Internal Medicine II, Uniklinik Ulm","Molecular Cardiology, Internal Medicine II, Uniklinik Ulm",2,0.95714,0.95793,0.10127,0.09788,0.69445,0.69278,0.47084,0.46602,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,bulk,bulk,,Germany,2023-08-01,Undetermined,Embryo,Whole Organism,All anatomical structures
25329,SRR25868071,SRX21589492,SRS18767065,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP4,GSM7749557,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP4,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749557,GSM7749557: sibCGFP4; Danio rerio; RNA Seq,GSM7749557 r1,GSM7749557,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP4_S46_L002_R1_001.fastq.gz WA-3548-sibCGFP4_S46_L002_R2_001.fastq.gz,fastq fastq,11996252984.0,39722692.0,GSM7749557 r1,0:151 1:151,A:3208564840;C:2791941387;G:2921724669;T:3073456372;N:565716,151,151,,,3208564840,2791941387,2921724669,3073456372,565716,SRX21589492,SRS18767065,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96224,0.96334,0.07442,0.07372,0.70595,0.70688,0.47053,0.46853,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25330,SRR25868072,SRX21589491,SRS18767064,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP3,GSM7749556,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749556,GSM7749556: sibCGFP3; Danio rerio; RNA Seq,GSM7749556 r1,GSM7749556,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP3_S45_L002_R1_001.fastq.gz WA-3548-sibCGFP3_S45_L002_R2_001.fastq.gz,fastq fastq,10113421300.0,33488150.0,GSM7749556 r1,0:151 1:151,A:2677217319;C:2366433560;G:2481164832;T:2588131881;N:473708,151,151,,,2677217319,2366433560,2481164832,2588131881,473708,SRX21589491,SRS18767064,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96295,0.96335,0.07275,0.07118,0.70654,0.7092,0.45672,0.44027,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25331,SRR25868073,SRX21589490,SRS18767063,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP2,GSM7749555,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749555,GSM7749555: sibCGFP2; Danio rerio; RNA Seq,GSM7749555 r1,GSM7749555,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP2_S44_L002_R1_001.fastq.gz WA-3548-sibCGFP2_S44_L002_R2_001.fastq.gz,fastq fastq,10142198578.0,33583439.0,GSM7749555 r1,0:151 1:151,A:2687719512;C:2375571494;G:2493046337;T:2585391111;N:470124,151,151,,,2687719512,2375571494,2493046337,2585391111,470124,SRX21589490,SRS18767063,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96241,0.96294,0.07398,0.07262,0.70524,0.70589,0.45777,0.46014,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25332,SRR25868074,SRX21589489,SRS18767062,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP1,GSM7749554,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749554,GSM7749554: sibCGFP1; Danio rerio; RNA Seq,GSM7749554 r1,GSM7749554,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP1_S43_L002_R1_001.fastq.gz WA-3548-sibCGFP1_S43_L002_R2_001.fastq.gz,fastq fastq,10994030650.0,36404075.0,GSM7749554 r1,0:151 1:151,A:2911908895;C:2573164804;G:2700790583;T:2807654156;N:512212,151,151,,,2911908895,2573164804,2700790583,2807654156,512212,SRX21589489,SRS18767062,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96119,0.96215,0.07361,0.07253,0.70632,0.7069,0.45503,0.45981,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25333,SRR25868075,SRX21589488,SRS18767059,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC4,GSM7749553,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC4,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749553,GSM7749553: sibC4; Danio rerio; RNA Seq,GSM7749553 r1,GSM7749553,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibC4_S42_L002_R1_001.fastq.gz WA-3548-sibC4_S42_L002_R2_001.fastq.gz,fastq fastq,11107320816.0,36779208.0,GSM7749553 r1,0:151 1:151,A:2945889871;C:2588267204;G:2719520712;T:2853118433;N:524596,151,151,,,2945889871,2588267204,2719520712,2853118433,524596,SRX21589488,SRS18767059,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96098,0.96213,0.07535,0.07463,0.70623,0.70749,0.42034,0.43255,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25334,SRR25868076,SRX21589487,SRS18767060,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC3,GSM7749552,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749552,GSM7749552: sibC3; Danio rerio; RNA Seq,GSM7749552 r1,GSM7749552,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibC3_S41_L002_R1_001.fastq.gz WA-3548-sibC3_S41_L002_R2_001.fastq.gz,fastq fastq,12566811014.0,41611957.0,GSM7749552 r1,0:151 1:151,A:3330340903;C:2960050871;G:3087690864;T:3188143295;N:585081,151,151,,,3330340903,2960050871,3087690864,3188143295,585081,SRX21589487,SRS18767060,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9619,0.96201,0.08592,0.08414,0.69581,0.69637,0.47091,0.47561,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25335,SRR25868077,SRX21589486,SRS18767057,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC2,GSM7749551,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749551,GSM7749551: sibC2; Danio rerio; RNA Seq,GSM7749551 r1,GSM7749551,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibC2_S40_L002_R1_001.fastq.gz WA-3548-sibC2_S40_L002_R2_001.fastq.gz,fastq fastq,9464242402.0,31338551.0,GSM7749551 r1,0:151 1:151,A:2497543137;C:2235078067;G:2319534414;T:2411649747;N:437037,151,151,,,2497543137,2235078067,2319534414,2411649747,437037,SRX21589486,SRS18767057,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96464,0.965,0.06696,0.06563,0.7138,0.71512,0.46359,0.46601,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25336,SRR25868078,SRX21589485,SRS18767061,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC1,GSM7749550,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749550,GSM7749550: sibC1; Danio rerio; RNA Seq,GSM7749550 r1,GSM7749550,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibC1_S39_L002_R1_001.fastq.gz WA-3548-sibC1_S39_L002_R2_001.fastq.gz,fastq fastq,11153872908.0,36933354.0,GSM7749550 r1,0:151 1:151,A:2966120106;C:2600333644;G:2710289968;T:2876608337;N:520853,151,151,,,2966120106,2600333644,2710289968,2876608337,520853,SRX21589485,SRS18767061,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96189,0.96306,0.07632,0.07512,0.70749,0.70818,0.46784,0.4683,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25337,SRR25868079,SRX21589484,SRS18767058,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP4,GSM7749549,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP4,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749549,GSM7749549: dmdGFP4; Danio rerio; RNA Seq,GSM7749549 r1,GSM7749549,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP4_S54_L002_R1_001.fastq.gz WA-3548-dmdGFP4_S54_L002_R2_001.fastq.gz,fastq fastq,6593937762.0,21834231.0,GSM7749549 r1,0:151 1:151,A:1745786828;C:1531704556;G:1637507801;T:1678632967;N:305610,151,151,,,1745786828,1531704556,1637507801,1678632967,305610,SRX21589484,SRS18767058,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9626,0.96282,0.08653,0.08533,0.70433,0.70636,0.47707,0.46994,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25338,SRR25868080,SRX21589483,SRS18767056,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP3,GSM7749548,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749548,GSM7749548: dmdGFP3; Danio rerio; RNA Seq,GSM7749548 r1,GSM7749548,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP3_S53_L002_R1_001.fastq.gz WA-3548-dmdGFP3_S53_L002_R2_001.fastq.gz,fastq fastq,9250573476.0,30631038.0,GSM7749548 r1,0:151 1:151,A:2485551140;C:2135752367;G:2259698711;T:2369143289;N:427969,151,151,,,2485551140,2135752367,2259698711,2369143289,427969,SRX21589483,SRS18767056,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96118,0.96196,0.0946,0.09271,0.69702,0.69834,0.47168,0.47515,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25339,SRR25868081,SRX21589482,SRS18767055,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP2,GSM7749547,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749547,GSM7749547: dmdGFP2; Danio rerio; RNA Seq,GSM7749547 r1,GSM7749547,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP2_S52_L002_R1_001.fastq.gz WA-3548-dmdGFP2_S52_L002_R2_001.fastq.gz,fastq fastq,8584886654.0,28426777.0,GSM7749547 r1,0:151 1:151,A:2310205296;C:1982936514;G:2071907465;T:2219441471;N:395908,151,151,,,2310205296,1982936514,2071907465,2219441471,395908,SRX21589482,SRS18767055,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9586,0.95966,0.09636,0.09473,0.69881,0.6997,0.47446,0.47409,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25340,SRR25868082,SRX21589481,SRS18767052,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP1,GSM7749546,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749546,GSM7749546: dmdGFP1; Danio rerio; RNA Seq,GSM7749546 r1,GSM7749546,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP1_S51_L002_R1_001.fastq.gz WA-3548-dmdGFP1_S51_L002_R2_001.fastq.gz,fastq fastq,7573189674.0,25076787.0,GSM7749546 r1,0:151 1:151,A:2025587174;C:1735604560;G:1848622101;T:1963022142;N:353697,151,151,,,2025587174,1735604560,1848622101,1963022142,353697,SRX21589481,SRS18767052,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.95942,0.96073,0.08752,0.08624,0.69863,0.69822,0.4733,0.47454,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25341,SRR25868083,SRX21589480,SRS18767054,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd4,GSM7749545,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd4,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749545,GSM7749545: dmd4; Danio rerio; RNA Seq,GSM7749545 r1,GSM7749545,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmd4_S50_L002_R1_001.fastq.gz WA-3548-dmd4_S50_L002_R2_001.fastq.gz,fastq fastq,9121652998.0,30204149.0,GSM7749545 r1,0:151 1:151,A:2438907102;C:2114952319;G:2225797925;T:2341561511;N:434141,151,151,,,2438907102,2114952319,2225797925,2341561511,434141,SRX21589480,SRS18767054,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.961,0.96258,0.08366,0.08276,0.69787,0.69856,0.47181,0.46112,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25342,SRR25868084,SRX21589479,SRS18767053,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd3,GSM7749544,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749544,GSM7749544: dmd3; Danio rerio; RNA Seq,GSM7749544 r1,GSM7749544,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmd3_S49_L002_R1_001.fastq.gz WA-3548-dmd3_S49_L002_R2_001.fastq.gz,fastq fastq,7896671538.0,26147919.0,GSM7749544 r1,0:151 1:151,A:2104101125;C:1828908837;G:1933039401;T:2030257090;N:365085,151,151,,,2104101125,1828908837,1933039401,2030257090,365085,SRX21589479,SRS18767053,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96014,0.96084,0.08575,0.08475,0.70082,0.70108,0.47254,0.47153,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25343,SRR25868085,SRX21589478,SRS18767051,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd2,GSM7749543,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749543,GSM7749543: dmd2; Danio rerio; RNA Seq,GSM7749543 r1,GSM7749543,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmd2_S48_L002_R1_001.fastq.gz WA-3548-dmd2_S48_L002_R2_001.fastq.gz,fastq fastq,9484006792.0,31403996.0,GSM7749543 r1,0:151 1:151,A:2518758838;C:2211640185;G:2303907076;T:2449259369;N:441324,151,151,,,2518758838,2211640185,2303907076,2449259369,441324,SRX21589478,SRS18767051,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96047,0.96128,0.09081,0.09031,0.69603,0.69605,0.46706,0.47077,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25344,SRR25868086,SRX21589477,SRS18767050,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd1,GSM7749542,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749542,GSM7749542: dmd1; Danio rerio; RNA Seq,GSM7749542 r1,GSM7749542,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmd1_S47_L002_R1_001.fastq.gz WA-3548-dmd1_S47_L002_R2_001.fastq.gz,fastq fastq,8411057568.0,27851184.0,GSM7749542 r1,0:151 1:151,A:2239146475;C:1963458820;G:2046268505;T:2161796444;N:387324,151,151,,,2239146475,1963458820,2046268505,2161796444,387324,SRX21589477,SRS18767050,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96292,0.96424,0.07952,0.07845,0.70473,0.70467,0.47569,0.47555,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25345,SRR25868018,SRX21589435,SRS18767008,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des trunk group 3,GSM7749541,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des trunk group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749541,GSM7749541: 20m des trunk group 3; Danio rerio; RNA Seq,GSM7749541 r1,GSM7749541,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_112_S23_L003_R1_001.fastq.gz P25101_112_S23_L003_R2_001.fastq.gz,fastq fastq,22210763348.0,73545574.0,GSM7749541 r1,0:151 1:151,A:5912051069;C:5198859790;G:5393563455;T:5706179211;N:109823,151,151,,,5912051069,5198859790,5393563455,5706179211,109823,SRX21589435,SRS18767008,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95876,0.95266,0.03675,0.03686,0.80085,0.80379,0.54105,0.54121,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25346,SRR25868019,SRX21589434,SRS18767007,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des trunk group 2,GSM7749540,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des trunk group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749540,GSM7749540: 20m des trunk group 2; Danio rerio; RNA Seq,GSM7749540 r1,GSM7749540,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_111_S22_L003_R1_001.fastq.gz P25101_111_S22_L003_R2_001.fastq.gz,fastq fastq,28432907098.0,94148699.0,GSM7749540 r1,0:151 1:151,A:7530352460;C:6691515017;G:7032193813;T:7178705133;N:140675,151,151,,,7530352460,6691515017,7032193813,7178705133,140675,SRX21589434,SRS18767007,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95304,0.94619,0.0303,0.03073,0.81288,0.81734,0.54159,0.529,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25347,SRR25868020,SRX21589433,SRS18767006,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des trunk group 1,GSM7749539,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des trunk group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749539,GSM7749539: 20m des trunk group 1; Danio rerio; RNA Seq,GSM7749539 r1,GSM7749539,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_110_S21_L003_R1_001.fastq.gz P25101_110_S21_L003_R2_001.fastq.gz,fastq fastq,22459067748.0,74367774.0,GSM7749539 r1,0:151 1:151,A:6073562522;C:5194312729;G:5517056007;T:5674024886;N:111604,151,151,,,6073562522,5194312729,5517056007,5674024886,111604,SRX21589433,SRS18767006,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95491,0.94862,0.03326,0.03384,0.8047,0.80949,0.54962,0.53948,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25348,SRR25868021,SRX21589432,SRS18767005,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt trunk group 3,GSM7749538,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt trunk group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749538,GSM7749538: 20m wt trunk group 3; Danio rerio; RNA Seq,GSM7749538 r1,GSM7749538,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_109_S20_L003_R1_001.fastq.gz P25101_109_S20_L003_R2_001.fastq.gz,fastq fastq,18161226926.0,60136513.0,GSM7749538 r1,0:151 1:151,A:4953172808;C:4151930418;G:4504584090;T:4551451588;N:88022,151,151,,,4953172808,4151930418,4504584090,4551451588,88022,SRX21589432,SRS18767005,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.94707,0.93454,0.03335,0.03308,0.80127,0.80708,0.56515,0.57038,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25349,SRR25868022,SRX21589431,SRS18767004,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt trunk group 2,GSM7749537,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt trunk group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749537,GSM7749537: 20m wt trunk group 2; Danio rerio; RNA Seq,GSM7749537 r1,GSM7749537,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_108_S19_L003_R1_001.fastq.gz P25101_108_S19_L003_R2_001.fastq.gz,fastq fastq,21168501250.0,70094375.0,GSM7749537 r1,0:151 1:151,A:5676216227;C:4922704340;G:5191762300;T:5377713558;N:104825,151,151,,,5676216227,4922704340,5191762300,5377713558,104825,SRX21589431,SRS18767004,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95544,0.94706,0.03451,0.03439,0.80998,0.81339,0.53843,0.50395,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25350,SRR25868023,SRX21589430,SRS18767003,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt trunk group 1,GSM7749536,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt trunk group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749536,GSM7749536: 20m wt trunk group 1; Danio rerio; RNA Seq,GSM7749536 r1,GSM7749536,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_107_S18_L003_R1_001.fastq.gz P25101_107_S18_L003_R2_001.fastq.gz,fastq fastq,21809914520.0,72218260.0,GSM7749536 r1,0:151 1:151,A:5826455436;C:5083672325;G:5302648618;T:5597031501;N:106640,151,151,,,5826455436,5083672325,5302648618,5597031501,106640,SRX21589430,SRS18767003,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.96041,0.95117,0.03443,0.03455,0.80598,0.80872,0.50583,0.4806,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25351,SRR25868024,SRX21589429,SRS18767002,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des EOM group 3,GSM7749535,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des EOM group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749535,GSM7749535: 20m des EOM group 3; Danio rerio; RNA Seq,GSM7749535 r1,GSM7749535,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_106_S17_L003_R1_001.fastq.gz P25101_106_S17_L003_R2_001.fastq.gz,fastq fastq,20778069912.0,68801556.0,GSM7749535 r1,0:151 1:151,A:5758676496;C:4631979297;G:4821571380;T:5565739517;N:103222,151,151,,,5758676496,4631979297,4821571380,5565739517,103222,SRX21589429,SRS18767002,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.9548,0.94562,0.05971,0.06026,0.75939,0.764,0.52511,0.52644,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25352,SRR25868025,SRX21589428,SRS18767001,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des EOM group 2,GSM7749534,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des EOM group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749534,GSM7749534: 20m des EOM group 2; Danio rerio; RNA Seq,GSM7749534 r1,GSM7749534,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_105_S16_L003_R1_001.fastq.gz P25101_105_S16_L003_R2_001.fastq.gz,fastq fastq,24114490412.0,79849306.0,GSM7749534 r1,0:151 1:151,A:6709705839;C:5352296650;G:5629660538;T:6422707312;N:120073,151,151,,,6709705839,5352296650,5629660538,6422707312,120073,SRX21589428,SRS18767001,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95523,0.9459,0.05709,0.05736,0.76047,0.76392,0.53211,0.53919,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25353,SRR25868026,SRX21589427,SRS18767000,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des EOM group 1,GSM7749533,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des EOM group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749533,GSM7749533: 20m des EOM group 1; Danio rerio; RNA Seq,GSM7749533 r1,GSM7749533,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_104_S15_L003_R1_001.fastq.gz P25101_104_S15_L003_R2_001.fastq.gz,fastq fastq,25533595358.0,84548329.0,GSM7749533 r1,0:151 1:151,A:7048075605;C:5727768890;G:5996832455;T:6760791489;N:126919,151,151,,,7048075605,5727768890,5996832455,6760791489,126919,SRX21589427,SRS18767000,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95578,0.94764,0.05575,0.05642,0.76449,0.76656,0.49924,0.52213,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25354,SRR25868027,SRX21589426,SRS18766999,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt EOM group 3,GSM7749532,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt EOM group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749532,GSM7749532: 20m wt EOM group 3; Danio rerio; RNA Seq,GSM7749532 r1,GSM7749532,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_103_S14_L003_R1_001.fastq.gz P25101_103_S14_L003_R2_001.fastq.gz,fastq fastq,20926207254.0,69292077.0,GSM7749532 r1,0:151 1:151,A:5774697444;C:4697440497;G:4906711794;T:5547254173;N:103346,151,151,,,5774697444,4697440497,4906711794,5547254173,103346,SRX21589426,SRS18766999,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95486,0.94747,0.05329,0.05381,0.76457,0.76725,0.53365,0.54294,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25355,SRR25868028,SRX21589425,SRS18766998,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt EOM group 2,GSM7749531,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt EOM group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749531,GSM7749531: 20m wt EOM group 2; Danio rerio; RNA Seq,GSM7749531 r1,GSM7749531,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_102_S13_L003_R2_001.fastq.gz P25101_102_S13_L003_R1_001.fastq.gz,fastq fastq,28078830218.0,92976259.0,GSM7749531 r1,0:151 1:151,A:7806960381;C:6272379496;G:6608688265;T:7390663010;N:139066,151,151,,,7806960381,6272379496,6608688265,7390663010,139066,SRX21589425,SRS18766998,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95324,0.94585,0.05086,0.05134,0.77315,0.77739,0.52072,0.52824,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25356,SRR25868029,SRX21589424,SRS18766997,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt EOM group 1,GSM7749530,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt EOM group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749530,GSM7749530: 20m wt EOM group 1; Danio rerio; RNA Seq,GSM7749530 r1,GSM7749530,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_101_S12_L003_R1_001.fastq.gz P25101_101_S12_L003_R2_001.fastq.gz,fastq fastq,20239673372.0,67018786.0,GSM7749530 r1,0:151 1:151,A:5648333279;C:4484295706;G:4758753699;T:5348189630;N:101058,151,151,,,5648333279,4484295706,4758753699,5348189630,101058,SRX21589424,SRS18766997,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95478,0.94612,0.05456,0.05574,0.76098,0.76668,0.50391,0.54818,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25357,SRR25868059,SRX21589476,SRS18767049,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des trunk group 3,GSM7749569,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des trunk group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749569,GSM7749569: des trunk group 3; Danio rerio; RNA Seq,GSM7749569 r1,GSM7749569,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_112_S16_L001_R1_001.fastq.gz P17251_112_S16_L001_R2_001.fastq.gz,fastq fastq,32975158332.0,109189266.0,GSM7749569 r1,0:151 1:151,A:8971397485;C:7542039111;G:8200961544;T:8260356002;N:404190,151,151,,,8971397485,7542039111,8200961544,8260356002,404190,SRX21589476,SRS18767049,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.9452,0.93318,0.03379,0.0337,0.80586,0.81485,0.56577,0.57552,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25358,SRR25868060,SRX21589475,SRS18767048,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des trunk group 2,GSM7749568,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des trunk group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749568,GSM7749568: des trunk group 2; Danio rerio; RNA Seq,GSM7749568 r1,GSM7749568,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_111_S15_L001_R1_001.fastq.gz P17251_111_S15_L001_R2_001.fastq.gz,fastq fastq,30771044854.0,101890877.0,GSM7749568 r1,0:151 1:151,A:8428723125;C:6962884900;G:7664589629;T:7714459134;N:388066,151,151,,,8428723125,6962884900,7664589629,7714459134,388066,SRX21589475,SRS18767048,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.94539,0.80414,0.03024,0.02542,0.8464,0.86281,0.50835,0.55329,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25359,SRR25868061,SRX21589474,SRS18767045,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des trunk group 1,GSM7749567,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des trunk group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749567,GSM7749567: des trunk group 1; Danio rerio; RNA Seq,GSM7749567 r1,GSM7749567,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_110_S14_L001_R1_001.fastq.gz P17251_110_S14_L001_R2_001.fastq.gz,fastq fastq,33874542116.0,112167358.0,GSM7749567 r1,0:151 1:151,A:8845255279;C:8046911900;G:8618139910;T:8363818933;N:416094,151,151,,,8845255279,8046911900,8618139910,8363818933,416094,SRX21589474,SRS18767045,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.94628,0.9369,0.02168,0.02198,0.83252,0.83816,0.5082,0.51978,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25360,SRR25868062,SRX21589473,SRS18767047,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt trunk group 3,GSM7749566,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt trunk group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749566,GSM7749566: wt trunk group 3; Danio rerio; RNA Seq,GSM7749566 r1,GSM7749566,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_109_S13_L001_R1_001.fastq.gz P17251_109_S13_L001_R2_001.fastq.gz,fastq fastq,34282805044.0,113519222.0,GSM7749566 r1,0:151 1:151,A:9124351621;C:8034310406;G:8391950458;T:8731771604;N:420955,151,151,,,9124351621,8034310406,8391950458,8731771604,420955,SRX21589473,SRS18767047,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.95625,0.95068,0.03255,0.03282,0.80555,0.81081,0.5875,0.58319,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25361,SRR25868063,SRX21589472,SRS18767046,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt trunk group 2,GSM7749565,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt trunk group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749565,GSM7749565: wt trunk group 2; Danio rerio; RNA Seq,GSM7749565 r1,GSM7749565,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_108_S12_L001_R1_001.fastq.gz P17251_108_S12_L001_R2_001.fastq.gz,fastq fastq,29439584536.0,97482068.0,GSM7749565 r1,0:151 1:151,A:7923205722;C:6779291710;G:7327163186;T:7409562179;N:361739,151,151,,,7923205722,6779291710,7327163186,7409562179,361739,SRX21589472,SRS18767046,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.94148,0.933,0.03555,0.03563,0.80562,0.81302,0.53017,0.5746,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25362,SRR25868064,SRX21589471,SRS18767044,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt trunk group 1,GSM7749564,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt trunk group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749564,GSM7749564: wt trunk group 1; Danio rerio; RNA Seq,GSM7749564 r1,GSM7749564,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_107_S11_L001_R1_001.fastq.gz P17251_107_S11_L001_R2_001.fastq.gz,fastq fastq,30984282826.0,102596963.0,GSM7749564 r1,0:151 1:151,A:8167387484;C:7329431316;G:7662021788;T:7825061355;N:380883,151,151,,,8167387484,7329431316,7662021788,7825061355,380883,SRX21589471,SRS18767044,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.94444,0.93765,0.03334,0.03351,0.80089,0.80535,0.56476,0.50751,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25363,SRR25868065,SRX21589470,SRS18767043,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des EOM group 3,GSM7749563,,source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des EOM group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749563,GSM7749563: des EOM group 3; Danio rerio; RNA Seq,GSM7749563 r1,GSM7749563,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_106_S10_L001_R1_001.fastq.gz P17251_106_S10_L001_R2_001.fastq.gz,fastq fastq,30795037848.0,101970324.0,GSM7749563 r1,0:151 1:151,A:8369479918;C:7035512003;G:7341959696;T:8047708763;N:377468,151,151,,,8369479918,7035512003,7341959696,8047708763,377468,SRX21589470,SRS18767043,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.95744,0.94806,0.06123,0.06213,0.75911,0.76382,0.53005,0.53206,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25364,SRR25868066,SRX21589469,SRS18767042,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des EOM group 2,GSM7749562,,source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des EOM group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749562,GSM7749562: des EOM group 2; Danio rerio; RNA Seq,GSM7749562 r1,GSM7749562,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_105_S9_L001_R1_001.fastq.gz P17251_105_S9_L001_R2_001.fastq.gz,fastq fastq,24388992708.0,80758254.0,GSM7749562 r1,0:151 1:151,A:6579219632;C:5651892239;G:6170251564;T:5987329579;N:299694,151,151,,,6579219632,5651892239,6170251564,5987329579,299694,SRX21589469,SRS18767042,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.96142,0.94783,0.02509,0.02601,0.81036,0.81913,0.52284,0.51505,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System