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
28490,SRR26319601,SRX22027740,SRS19100857,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Treatment,CX3 for transcriptome 3,CX3,,strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.67 E|treatment:Treatment Group|BioSampleModel:Model organism or animal,,,,,,,,,ALST3 for transcriptome 3,CX3 for transcriptome 3,CX3 for transcriptome 3,CX3 for transcriptome 3,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0006_good_1.fq.gz Unknown_AY803-03T0006_good_2.fq.gz,fastq fastq,6255596356.0,20929531.0,Unknown AY803 03T0006 good 1.fq.gz,0:149.44 1:149.44,A:1657365560;C:1463722268;G:1467057724;T:1667269298;N:181506,149,149,,,1657365560,1463722268,1467057724,1667269298,181506,SRX22027740,SRS19100857,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.89228,0.91654,0.09286,0.09714,0.6588,0.65604,0.4631,0.45773,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28491,SRR26319602,SRX22027739,SRS19100854,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Treatment,CX2 for transcriptome 2,CX2,,strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.66 E|treatment:Treatment Group|BioSampleModel:Model organism or animal,,,,,,,,,ALST2 for transcriptome 2,CX2 for transcriptome 2,CX2 for transcriptome 2,CX2 for transcriptome 2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0005_good_1.fq.gz Unknown_AY803-03T0005_good_2.fq.gz,fastq fastq,6598066464.0,22061446.0,Unknown AY803 03T0005 good 1.fq.gz,0:149.54 1:149.54,A:1747291499;C:1543289262;G:1549193118;T:1758088368;N:204217,149,149,,,1747291499,1543289262,1549193118,1758088368,204217,SRX22027739,SRS19100854,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.88949,0.92148,0.08893,0.0947,0.65596,0.65228,0.46045,0.47087,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28492,SRR26319603,SRX22027738,SRS19100853,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Treatment,CX1 for transcriptome 1,CX1,,strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.65 E|treatment:Treatment Group|BioSampleModel:Model organism or animal,,,,,,,,,ALST1 for transcriptome 1,CX1 for transcriptome 1,CX1 for transcriptome 1,CX1 for transcriptome 1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0004_good_1.fq.gz Unknown_AY803-03T0004_good_2.fq.gz,fastq fastq,6478923586.0,21662443.0,Unknown AY803 03T0004 good 1.fq.gz,0:149.54 1:149.54,A:1712718473;C:1518937459;G:1523570227;T:1723510437;N:186990,149,149,,,1712718473,1518937459,1523570227,1723510437,186990,SRX22027738,SRS19100853,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.89423,0.9176,0.08944,0.09254,0.6575,0.65458,0.4693,0.46842,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28493,SRR26319604,SRX22027737,SRS19100856,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Control,con3 for transcriptome 3,con3,,strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.64 E|treatment:Control Group|BioSampleModel:Model organism or animal,,,,,,,,,con3 for transcriptome 3,con3 for transcriptome 3,con3 for transcriptome 3,con3 for transcriptome 3,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0003_good_2.fq.gz Unknown_AY803-03T0003_good_1.fq.gz,fastq fastq,6341537566.0,21218597.0,Unknown AY803 03T0003 good 1.fq.gz,0:149.43 1:149.43,A:1679811754;C:1483631833;G:1489430825;T:1688482904;N:180250,149,149,,,1679811754,1483631833,1489430825,1688482904,180250,SRX22027737,SRS19100856,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.88245,0.91856,0.09069,0.09654,0.66253,0.65817,0.46245,0.46336,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28494,SRR26319605,SRX22027736,SRS19100855,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Control,con2 for transcriptome 2,con2,,strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.63 E|treatment:Control Group|BioSampleModel:Model organism or animal,,,,,,,,,con2 for transcriptome 2,con2 for transcriptome 2,con2 for transcriptome 2,con2 for transcriptome 2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0002_good_2.fq.gz Unknown_AY803-03T0002_good_1.fq.gz,fastq fastq,5709771178.0,19100144.0,Unknown AY803 03T0002 good 1.fq.gz,0:149.47 1:149.47,A:1505730979;C:1342843084;G:1346105868;T:1514941964;N:149283,149,149,,,1505730979,1342843084,1346105868,1514941964,149283,SRX22027736,SRS19100855,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.8924,0.91903,0.09155,0.09604,0.65902,0.65593,0.4634,0.46028,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28495,SRR26319606,SRX22027735,SRS19100852,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Control,con1 for transcriptome 1,con1,,strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.62 E|treatment:Control Group|BioSampleModel:Model organism or animal,,,,,,,,,con1 for transcriptome 1,con1 for transcriptome 1,con1 for transcriptome 1,con1 for transcriptome 1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0001_good_1.fq.gz Unknown_AY803-03T0001_good_2.fq.gz,fastq fastq,6544586118.0,21872265.0,Unknown AY803 03T0001 good 1.fq.gz,0:149.61 1:149.61,A:1731179229;C:1528367346;G:1541103688;T:1743735521;N:200334,149,149,,,1731179229,1528367346,1541103688,1743735521,200334,SRX22027735,SRS19100852,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.87588,0.92739,0.08683,0.09494,0.65711,0.6504,0.46774,0.47072,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
36278,SRR352486,SRX100938,SRS266977,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,3P Seq Adult,GSM813764,,source name:mixed gender adults|tissue:whole adult|developmental stage:mixed gender adults|genotype:wt,3P Seq Adult,Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924,mixed gender adults,For adult fish  anesthetized fish were homogenized in the TissueRuptor Qiagen. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,tissue:whole adult|developmental stage:mixed gender adults|genotype:wt,GSM813764,GSM813764: 3P Seq Adult,GSM813764: 3P Seq Adult,GSM813764: 3P Seq Adult,1,,GEO Accession:GSM813764,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,3P_Seq_Adult.fastq,fastq,824962572.0,22915627.0,GSM813764 1,0:36,A:230176177;C:144743199;G:130818857;T:314618483;N:4605856,36,,,,230176177,144743199,130818857,314618483,4605856,SRX100938,SRS266977,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.64306,,0.03985,,0.78102,,0.46237,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Adult,Adult,Whole Organism,All anatomical structures
36279,SRR352485,SRX100937,SRS266976,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,3P Seq 72 hpf,GSM813763,,tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf,3P Seq 72 hpf,Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924,whole embryo at 72 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:72 hpf,GSM813763,GSM813763: 3P Seq 72 hpf,GSM813763: 3P Seq 72 hpf,GSM813763: 3P Seq 72 hpf,1,,GEO Accession:GSM813763,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,3P_Seq_72hpf.fastq,fastq,875542968.0,24320638.0,GSM813763 1,0:36,A:246098313;C:139311840;G:129654215;T:353566279;N:6912321,36,,,,246098313,139311840,129654215,353566279,6912321,SRX100937,SRS266976,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.72092,,0.09355,,0.7601,,0.4422,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Larval,Larval,Whole Organism,All anatomical structures
36280,SRR352484,SRX100936,SRS266975,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,3P Seq 24 hpf,GSM813762,,tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf,3P Seq 24 hpf,Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924,whole embryo at 24 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:24 hpf,GSM813762,GSM813762: 3P Seq 24 hpf,GSM813762: 3P Seq 24 hpf,GSM813762: 3P Seq 24 hpf,1,,GEO Accession:GSM813762,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,3P_Seq_24hpf.fastq,fastq,951095592.0,26419322.0,GSM813762 1,0:36,A:261158914;C:169001356;G:163312440;T:350565754;N:7057128,36,,,,261158914,169001356,163312440,350565754,7057128,SRX100936,SRS266975,SRA047033,GEO,Whitehead Institute for Biomedical Research,,,,,,,,,,,,B,,usable mapping rate,illumina,early_illumina,3prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
36281,SRR352482,SRX100935,SRS266974,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,Strand specific RNA Seq 72 hpf,GSM813761,,tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf,Strand specific RNA Seq 72 hpf,Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.,whole embryo at 72 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:72 hpf,GSM813761,GSM813761: Strand specific RNA Seq 72 hpf,GSM813761: Strand specific RNA Seq 72 hpf,GSM813761: Strand specific RNA Seq 72 hpf,1,,GEO Accession:GSM813761,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,RNA_Seq_72hpf.1.fastq,fastq,734147136.0,20392976.0,GSM813761 1,0:36,A:175662892;C:172216317;G:208650086;T:171852136;N:5765705,36,,,,175662892,172216317,208650086,171852136,5765705,SRX100935,SRS266974,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.4603,,0.10593,,0.88274,,0.59195,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Larval,Larval,Whole Organism,All anatomical structures
36282,SRR352483,SRX100935,SRS266974,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,Strand specific RNA Seq 72 hpf,GSM813761,,tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf,Strand specific RNA Seq 72 hpf,Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.,whole embryo at 72 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:72 hpf,GSM813761,GSM813761: Strand specific RNA Seq 72 hpf,GSM813761: Strand specific RNA Seq 72 hpf,GSM813761: Strand specific RNA Seq 72 hpf,1,,GEO Accession:GSM813761,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,RNA_Seq_72hpf.2.fastq,fastq,924879168.0,25691088.0,GSM813761 2,0:36,A:218871678;C:217000200;G:266487098;T:214411336;N:8108856,36,,,,218871678,217000200,266487098,214411336,8108856,SRX100935,SRS266974,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.47296,,0.10988,,0.86397,,0.59423,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Larval,Larval,Whole Organism,All anatomical structures
36283,SRR352480,SRX100934,SRS266973,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,Strand specific RNA Seq 24 hpf,GSM813760,,tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf,Strand specific RNA Seq 24 hpf,Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.,whole embryo at 24 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:24 hpf,GSM813760,GSM813760: Strand specific RNA Seq 24 hpf,GSM813760: Strand specific RNA Seq 24 hpf,GSM813760: Strand specific RNA Seq 24 hpf,1,,GEO Accession:GSM813760,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,RNA_Seq_24hpf.1.fastq,fastq,759129588.0,21086933.0,GSM813760 1,0:36,A:169759696;C:187766678;G:221392768;T:174382883;N:5827563,36,,,,169759696,187766678,221392768,174382883,5827563,SRX100934,SRS266973,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.52959,,0.10037,,0.87014,,0.61896,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
36284,SRR352481,SRX100934,SRS266973,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,Strand specific RNA Seq 24 hpf,GSM813760,,tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf,Strand specific RNA Seq 24 hpf,Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.,whole embryo at 24 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:24 hpf,GSM813760,GSM813760: Strand specific RNA Seq 24 hpf,GSM813760: Strand specific RNA Seq 24 hpf,GSM813760: Strand specific RNA Seq 24 hpf,1,,GEO Accession:GSM813760,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,RNA_Seq_24hpf.2.fastq,fastq,916505136.0,25458476.0,GSM813760 2,0:36,A:203678661;C:227621613;G:269472018;T:207401580;N:8331264,36,,,,203678661,227621613,269472018,207401580,8331264,SRX100934,SRS266973,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.54008,,0.10064,,0.85425,,0.61991,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
36731,SRR836199,SRX272888,SRS417394,SRP021915,PRJNA200706,Ribosome Profiling over a Zebrafish Developmental Timecourse,GSE46512,Transcriptome Analysis,To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf,,pubmed:23698349,,20120724 RPF Seq 5dpf,GSM1131537,,tissue:Whole embryos|developmental stage:5 dpf molecule:ribosome footprinted RNA,20120724 RPF Seq 5dpf,Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes,Whole embryos,Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995,developmental stage:5 dpf molecule:ribosome footprinted RNA,GSM1131537,GSM1131537: 20120724 RPF Seq 5dpf; Danio rerio; RNA Seq,GSM1131537 1,,1,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,GEO Accession:GSM1131537,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021915,,,20120724_RPF-Seq_5dpf.fastq.gz,fastq,5339394852.0,121349883.0,GSM1131537 r1,0:44,A:993131212;C:1552513636;G:1792926993;T:1000757523;N:65488,44,,,,993131212,1552513636,1792926993,1000757523,65488,SRX272888,SRS417394,SRA075002,GEO,"Schier, Dept of Molecular and Cellular Biology, Harvard University",1,0.04708,,0.00988,,0.99774,,0.7502,,44,,B,,usable mapping rate,illumina,hiseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2013-04-30,Larval,Larval,Whole Organism,All anatomical structures
36732,SRR836198,SRX272887,SRS417393,SRP021915,PRJNA200706,Ribosome Profiling over a Zebrafish Developmental Timecourse,GSE46512,Transcriptome Analysis,To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf,,pubmed:23698349,,20120724 RPF Seq 28hpf,GSM1131536,,tissue:Whole embryos|developmental stage:28 hpf molecule:ribosome footprinted RNA,20120724 RPF Seq 28hpf,Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes,Whole embryos,Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995,developmental stage:28 hpf molecule:ribosome footprinted RNA,GSM1131536,GSM1131536: 20120724 RPF Seq 28hpf; Danio rerio; RNA Seq,GSM1131536 1,,1,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,GEO Accession:GSM1131536,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021915,,,20120724_RPF-Seq_28hpf.fastq.gz,fastq,5844769480.0,132835670.0,GSM1131536 r1,0:44,A:967687923;C:1803414766;G:2048220630;T:1024594100;N:852061,44,,,,967687923,1803414766,2048220630,1024594100,852061,SRX272887,SRS417393,SRA075002,GEO,"Schier, Dept of Molecular and Cellular Biology, Harvard University",1,0.054,,0.00377,,0.99762,,0.77752,,44,,B,,usable mapping rate,illumina,hiseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2013-04-30,Pharyngula,Embryo,Whole Organism,All anatomical structures
36733,SRR836197,SRX272886,SRS417392,SRP021915,PRJNA200706,Ribosome Profiling over a Zebrafish Developmental Timecourse,GSE46512,Transcriptome Analysis,To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf,,pubmed:23698349,,20120724 RPF Seq Bud,GSM1131535,,tissue:Whole embryos|developmental stage:Bud|strain:TL/AB|target molecule:ribosome footprinted RNA,20120724 RPF Seq Bud,Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes,Whole embryos,Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995,developmental stage:Bud|strain:TL/AB|target molecule:ribosome footprinted RNA,GSM1131535,GSM1131535: 20120724 RPF Seq Bud; Danio rerio; RNA Seq,GSM1131535 1,,1,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,GEO Accession:GSM1131535,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021915,,,20120724_RPF-Seq_Bud.fastq.gz,fastq,5245678988.0,119219977.0,GSM1131535 r1,0:44,A:785136766;C:1705642298;G:1892015387;T:862815185;N:69352,44,,,,785136766,1705642298,1892015387,862815185,69352,SRX272886,SRS417392,SRA075002,GEO,"Schier, Dept of Molecular and Cellular Biology, Harvard University",1,0.0214,,0.00105,,0.99823,,0.906,,44,,B,,usable mapping rate,illumina,hiseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2013-04-30,Undetermined,Embryo,Whole Organism,All anatomical structures
36734,SRR836196,SRX272885,SRS417391,SRP021915,PRJNA200706,Ribosome Profiling over a Zebrafish Developmental Timecourse,GSE46512,Transcriptome Analysis,To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf,,pubmed:23698349,,20120724 RPF Seq Shield,GSM1131534,,tissue:Whole embryos|developmental stage:Shield|strain:TL/AB|target molecule:ribosome footprinted RNA,20120724 RPF Seq Shield,Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes,Whole embryos,Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995,developmental stage:Shield|strain:TL/AB|target molecule:ribosome footprinted RNA,GSM1131534,GSM1131534: 20120724 RPF Seq Shield; Danio rerio; RNA Seq,GSM1131534 1,,1,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,GEO Accession:GSM1131534,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021915,,,20120724_RPF-Seq_Shield.fastq.gz,fastq,5407148516.0,122889739.0,GSM1131534 r1,0:44,A:1112688703;C:1598204601;G:1639649897;T:1055648833;N:956482,44,,,,1112688703,1598204601,1639649897,1055648833,956482,SRX272885,SRS417391,SRA075002,GEO,"Schier, Dept of Molecular and Cellular Biology, Harvard University",1,0.01533,,0.0016,,0.99864,,0.73416,,44,,B,,usable mapping rate,illumina,hiseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2013-04-30,Gastrula,Embryo,Whole Organism,All anatomical structures
36735,SRR836195,SRX272884,SRS417390,SRP021915,PRJNA200706,Ribosome Profiling over a Zebrafish Developmental Timecourse,GSE46512,Transcriptome Analysis,To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf,,pubmed:23698349,,20120724 RPF Seq Dome,GSM1131533,,tissue:Whole embryos|developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA,20120724 RPF Seq Dome,Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes,Whole embryos,Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995,developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA,GSM1131533,GSM1131533: 20120724 RPF Seq Dome; Danio rerio; RNA Seq,GSM1131533 1,,1,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,GEO Accession:GSM1131533,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021915,,,20120724_RPF-Seq_Dome.fastq.gz,fastq,5455941832.0,123998678.0,GSM1131533 r1,0:44,A:1174530251;C:1596486361;G:1605087499;T:1077423125;N:2414596,44,,,,1174530251,1596486361,1605087499,1077423125,2414596,SRX272884,SRS417390,SRA075002,GEO,"Schier, Dept of Molecular and Cellular Biology, Harvard University",1,0.00739,,0.0007,,0.99898,,0.86907,,44,,T,,under 1.2% mapping rate,illumina,hiseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2013-04-30,Blastula,Embryo,Whole Organism,All anatomical structures
36736,SRR836194,SRX272883,SRS417389,SRP021915,PRJNA200706,Ribosome Profiling over a Zebrafish Developmental Timecourse,GSE46512,Transcriptome Analysis,To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf,,pubmed:23698349,,20120724 RPF Seq 1KCell,GSM1131532,,tissue:Whole embryos|developmental stage:1k cells|strain:TL/AB|target molecule:ribosome footprinted RNA,20120724 RPF Seq 1KCell,Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes,Whole embryos,Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995,developmental stage:1k cells|strain:TL/AB|target molecule:ribosome footprinted RNA,GSM1131532,GSM1131532: 20120724 RPF Seq 1KCell; Danio rerio; RNA Seq,GSM1131532 1,,1,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,GEO Accession:GSM1131532,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021915,,,20120724_RPF-Seq_1KCell.fastq.gz,fastq,6177670620.0,140401605.0,GSM1131532 r1,0:44,A:1115906097;C:1874096579;G:1974799887;T:1211772717;N:1095340,44,,,,1115906097,1874096579,1974799887,1211772717,1095340,SRX272883,SRS417389,SRA075002,GEO,"Schier, Dept of Molecular and Cellular Biology, Harvard University",1,0.02237,,0.00392,,0.99847,,0.87194,,44,,B,,usable mapping rate,illumina,hiseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2013-04-30,Blastula,Embryo,Whole Organism,All anatomical structures
36737,SRR836193,SRX272882,SRS417388,SRP021915,PRJNA200706,Ribosome Profiling over a Zebrafish Developmental Timecourse,GSE46512,Transcriptome Analysis,To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf,,pubmed:23698349,,20120724 RPF Seq 256Cell,GSM1131531,,tissue:Whole embryos|developmental stage:256 cells|strain:TL/AB|target molecule:ribosome footprinted RNA,20120724 RPF Seq 256Cell,Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes,Whole embryos,Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995,developmental stage:256 cells|strain:TL/AB|target molecule:ribosome footprinted RNA,GSM1131531,GSM1131531: 20120724 RPF Seq 256Cell; Danio rerio; RNA Seq,GSM1131531 1,,1,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,GEO Accession:GSM1131531,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021915,,,20120724_RPF-Seq_256Cell.fastq.gz,fastq,5883566700.0,133717425.0,GSM1131531 r1,0:44,A:1010263447;C:1822722383;G:1960819573;T:1088614485;N:1146812,44,,,,1010263447,1822722383,1960819573,1088614485,1146812,SRX272882,SRS417388,SRA075002,GEO,"Schier, Dept of Molecular and Cellular Biology, Harvard University",1,0.02862,,0.0036,,0.99837,,0.90559,,44,,B,,usable mapping rate,illumina,hiseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2013-04-30,Blastula,Embryo,Whole Organism,All anatomical structures
36738,SRR836192,SRX272881,SRS417387,SRP021915,PRJNA200706,Ribosome Profiling over a Zebrafish Developmental Timecourse,GSE46512,Transcriptome Analysis,To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf,,pubmed:23698349,,20120724 RPF Seq 2 4Cell,GSM1131530,,tissue:Whole embryos|developmental stage:2 4 cells|strain:TL/AB|target molecule:ribosome footprinted RNA,20120724 RPF Seq 2 4Cell,Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes,Whole embryos,Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995,developmental stage:2 4 cells|strain:TL/AB|target molecule:ribosome footprinted RNA,GSM1131530,GSM1131530: 20120724 RPF Seq 2 4Cell; Danio rerio; RNA Seq,GSM1131530 1,,1,Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 μg/ml cycloheximide with added 0.5% Triton X 100  500 μg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4°C  and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C  then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C  and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011,GEO Accession:GSM1131530,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021915,,,20120724_RPF-Seq_2-4Cell.fastq.gz,fastq,1568173420.0,35640305.0,GSM1131530 r1,0:44,A:256220962;C:489258424;G:538563811;T:283859833;N:270390,44,,,,256220962,489258424,538563811,283859833,270390,SRX272881,SRS417387,SRA075002,GEO,"Schier, Dept of Molecular and Cellular Biology, Harvard University",1,0.0297,,0.00558,,0.99821,,0.89066,,44,,B,,usable mapping rate,illumina,hiseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2013-04-30,Cleavage,Embryo,Whole Organism,All anatomical structures
75414,SRR24517729,SRX20302027,SRS17627883,SRP437283,PRJNA971676,zebrafish kiss genes knockouts deep sequencing,PRJNA971676,Other,Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.,,,,RNA seq of zebrafish:5dpf larvae kiss1kiss2DKO Replicate2,zebrafish AO149 01T0008,,strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss1 and kiss2 double knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: larvae,RNA Seq for zebrafish kiss1kiss2DKO larvae 2,RNA Seq for zebrafish kiss1kiss2DKO larvae 2,RNA Seq   zebrafish kiss1kiss2DKO larvae 2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP437283,,,Unknown_AO149-01T0008_good_1.fq.gz Unknown_AO149-01T0008_good_2.fq.gz,fastq fastq,6912158300.0,23173882.0,Unknown AO149 01T0008 good 1.fq.gz,0:149.14 1:149.14,A:1796529490;C:1649628994;G:1669079817;T:1796880198;N:39801,149,149,,,1796529490,1649628994,1669079817,1796880198,39801,SRX20302027,SRS17627883,SRA1636880,Soochow University|Medical College,Soochow University,2,0.95632,0.95592,0.06085,0.06019,0.66515,0.66563,0.47686,0.47575,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-05-11,Larval,Larval,Whole Organism,All anatomical structures
75415,SRR24517730,SRX20302026,SRS17627882,SRP437283,PRJNA971676,zebrafish kiss genes knockouts deep sequencing,PRJNA971676,Other,Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.,,,,RNA seq of zebrafish:5dpf larvae kiss1kiss2DKO Replicate1,zebrafish AO149 01T0007,,strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss1 and kiss2 double knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: larvae,RNA Seq for zebrafish kiss1kiss2DKO larvae 1,RNA Seq  for zebrafish kiss1kiss2DKO larvae 1,RNA Seq   zebrafish kiss1kiss2DKO larvae 1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP437283,,,Unknown_AO149-01T0007_good_1.fq.gz Unknown_AO149-01T0007_good_2.fq.gz,fastq fastq,8005311792.0,26909041.0,Unknown AO149 01T0007 good 1.fq.gz,0:148.75 1:148.75,A:2077441584;C:1913582326;G:1934120275;T:2080121870;N:45737,148,148,,,2077441584,1913582326,1934120275,2080121870,45737,SRX20302026,SRS17627882,SRA1636880,Soochow University|Medical College,Soochow University,2,0.9522,0.95194,0.06345,0.06296,0.65691,0.65744,0.48074,0.48185,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-05-11,Larval,Larval,Whole Organism,All anatomical structures
75416,SRR24517731,SRX20302025,SRS17627881,SRP437283,PRJNA971676,zebrafish kiss genes knockouts deep sequencing,PRJNA971676,Other,Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.,,,,RNA seq of zebrafish:5dpf larvae kiss2KO Replicate2,zebrafish AO149 01T0006,,strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss2 knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: larvae,RNA Seq for zebrafish kiss2KO larvae 2,RNA Seq for zebrafish kiss2KO  larvae 2,RNA Seq  zebrafish kiss2KO  larvae 2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP437283,,,Unknown_AO149-01T0006_good_1.fq.gz Unknown_AO149-01T0006_good_2.fq.gz,fastq fastq,7638089446.0,25894588.0,Unknown AO149 01T0006 good 1.fq.gz,0:147.48 1:147.48,A:2051138070;C:1759130157;G:1773591862;T:2054190526;N:38831,147,147,,,2051138070,1759130157,1773591862,2054190526,38831,SRX20302025,SRS17627881,SRA1636880,Soochow University|Medical College,Soochow University,2,0.94967,0.94887,0.08556,0.08576,0.64898,0.64954,0.47984,0.48067,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-05-11,Larval,Larval,Whole Organism,All anatomical structures
75417,SRR24517732,SRX20302024,SRS17627879,SRP437283,PRJNA971676,zebrafish kiss genes knockouts deep sequencing,PRJNA971676,Other,Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.,,,,RNA seq of zebrafish:5dpf larvae kiss2KO Replicate1,zebrafish AO149 01T0005,,strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss2 knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: larvae,RNA Seq for zebrafish kiss2KO larvae 1,RNA Seq for  zebrafish  kiss2KO  larvae 1,RNA Seq   zebrafish  kiss2KO  larvae 1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP437283,,,Unknown_AO149-01T0005_good_1.fq.gz Unknown_AO149-01T0005_good_2.fq.gz,fastq fastq,7054134954.0,23687508.0,Unknown AO149 01T0005 good 1.fq.gz,0:148.90 1:148.90,A:1848389593;C:1667928954;G:1687707295;T:1850068763;N:40349,148,148,,,1848389593,1667928954,1687707295,1850068763,40349,SRX20302024,SRS17627879,SRA1636880,Soochow University|Medical College,Soochow University,2,0.94976,0.95007,0.07472,0.07458,0.65299,0.65324,0.48045,0.47909,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-05-11,Larval,Larval,Whole Organism,All anatomical structures
75418,SRR24517733,SRX20302023,SRS17627880,SRP437283,PRJNA971676,zebrafish kiss genes knockouts deep sequencing,PRJNA971676,Other,Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.,,,,RNA seq of zebrafish:5dpf larvae kiss1KO Replicate2,zebrafish AO149 01T0004,,strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss1 knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: larvae,RNA Seq for zebrafish kiss1KO larvae 2,RNA Seq for  zebrafish  kiss1KO  larvae 2,RNA Seq   zebrafish  kiss1KO  larvae 2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP437283,,,Unknown_AO149-01T0004_good_1.fq.gz Unknown_AO149-01T0004_good_2.fq.gz,fastq fastq,5814495346.0,19499621.0,Unknown AO149 01T0004 good 1.fq.gz,0:149.09 1:149.09,A:1528388873;C:1369910846;G:1386794007;T:1529368087;N:33533,149,149,,,1528388873,1369910846,1386794007,1529368087,33533,SRX20302023,SRS17627880,SRA1636880,Soochow University|Medical College,Soochow University,2,0.94765,0.94711,0.07972,0.07979,0.65283,0.65397,0.48362,0.48203,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-05-11,Larval,Larval,Whole Organism,All anatomical structures
75419,SRR24517734,SRX20302022,SRS17627877,SRP437283,PRJNA971676,zebrafish kiss genes knockouts deep sequencing,PRJNA971676,Other,Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.,,,,RNA seq of zebrafish:5dpf larvae kiss1KO Replicate1,zebrafish AO149 01T0003,,strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss1 knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: larvae,RNA Seq for zebrafish kiss1KO larvae 1,RNA Seq for  zebrafish kiss1KO larvae 1,RNA Seq   zebrafish kiss1KO larvae 1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP437283,,,Unknown_AO149-01T0003_good_1.fq.gz Unknown_AO149-01T0003_good_2.fq.gz,fastq fastq,6174484352.0,20748774.0,Unknown AO149 01T0003 good 1.fq.gz,0:148.79 1:148.79,A:1629263285;C:1446858897;G:1467609266;T:1630717493;N:35411,148,148,,,1629263285,1446858897,1467609266,1630717493,35411,SRX20302022,SRS17627877,SRA1636880,Soochow University|Medical College,Soochow University,2,0.94831,0.94853,0.07898,0.07866,0.65295,0.65419,0.47605,0.47682,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-05-11,Larval,Larval,Whole Organism,All anatomical structures
75420,SRR24517735,SRX20302021,SRS17627878,SRP437283,PRJNA971676,zebrafish kiss genes knockouts deep sequencing,PRJNA971676,Other,Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.,,,,RNA seq of zebrafish:5dpf larvae wt Replicate2,zebrafish AO149 01T0002,,strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:WT|geo loc name:China: Suzhou|sample type:whole organism|Replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: larvae,RNA Seq for zebrafish WT larvae 2,RNA Seq  for zebrafish WT  larvae 2,RNA Seq   zebrafish WT  larvae 2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP437283,,,Unknown_AO149-01T0002_good_1.fq.gz Unknown_AO149-01T0002_good_2.fq.gz,fastq fastq,6059983436.0,20361363.0,Unknown AO149 01T0002 good 1.fq.gz,0:148.81 1:148.81,A:1608075382;C:1408291949;G:1433236990;T:1610344312;N:34803,148,148,,,1608075382,1408291949,1433236990,1610344312,34803,SRX20302021,SRS17627878,SRA1636880,Soochow University|Medical College,Soochow University,2,0.9529,0.95334,0.07296,0.07315,0.65435,0.65247,0.49743,0.47334,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-05-11,Larval,Larval,Whole Organism,All anatomical structures
75421,SRR24517736,SRX20302020,SRS17627876,SRP437283,PRJNA971676,zebrafish kiss genes knockouts deep sequencing,PRJNA971676,Other,Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.,,,,RNA seq of zebrafish:5dpf larvae wt Replicate1,zebrafish AO149 01T0001,,strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:WT|geo loc name:China: Suzhou|sample type:whole organism|Replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: larvae,RNA Seq for zebrafish WT larvae 1,RNA Seq for zebrafish WT larvae 1,RNA Seq   zebrafish WT larvae 1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP437283,,,Unknown_AO149-01T0001_good_1.fq.gz Unknown_AO149-01T0001_good_2.fq.gz,fastq fastq,6809997812.0,22853255.0,Unknown AO149 01T0001 good 1.fq.gz,0:148.99 1:148.99,A:1813360438;C:1582845212;G:1601287701;T:1812465242;N:39219,148,148,,,1813360438,1582845212,1601287701,1812465242,39219,SRX20302020,SRS17627876,SRA1636880,Soochow University|Medical College,Soochow University,2,0.94825,0.94824,0.087,0.08724,0.64695,0.64715,0.49206,0.493,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-05-11,Larval,Larval,Whole Organism,All anatomical structures