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
10056,ERR4691987,ERX4613068,ERS5216074,ERP124560,PRJEB40865,RNA seq of zebrafish adult MCU mutant hearts,ena-STUDY-UCLA-16-10-2020-22:30:44:295-390,Other,We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16,,,zebrafish adult heart RNA,SAMEA7457891,UCLA,ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457891|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 2|common name:zebrafish|dev stage:adult|sample name:mcu mutant 2|scientific name:Danio rerio|tissue type:heart,,,,,,,,,Illumina HiSeq 3000 sequencing,ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 3000,,ERP124560,Illumina HiSeq 3000 sequencing,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21,MCU_2.fastq.gz,fastq,1291626898.0,35072619.0,ena RUN UCLA 16 10 2020 22:30:43:819 4,0:36.83 1:0,A:364596432;C:305716590;G:295397140;T:324498501;N:1418235,36,0,,,364596432,305716590,295397140,324498501,1418235,ERX4613068,ERS5216074,ERA2987364,European Nucleotide Archive,"University of California, Los Angeles, USA",1,0.93311,,0.08182,,0.75852,,0.54813,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2020-10-16,Adult,Adult,Heart,Cardiovascular System
10057,ERR4691986,ERX4613067,ERS5216073,ERP124560,PRJEB40865,RNA seq of zebrafish adult MCU mutant hearts,ena-STUDY-UCLA-16-10-2020-22:30:44:295-390,Other,We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16,,,zebrafish adult heart RNA,SAMEA7457890,UCLA,ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457890|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 1|common name:zebrafish|dev stage:adult|sample name:mcu mutant 1|scientific name:Danio rerio|tissue type:heart,,,,,,,,,Illumina HiSeq 3000 sequencing,ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 3000,,ERP124560,Illumina HiSeq 3000 sequencing,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21,MCU_1.fastq.gz,fastq,1236033124.0,33559740.0,ena RUN UCLA 16 10 2020 22:30:43:819 3,0:36.83 1:0,A:348518065;C:293502111;G:279181983;T:313506799;N:1324166,36,0,,,348518065,293502111,279181983,313506799,1324166,ERX4613067,ERS5216073,ERA2987364,European Nucleotide Archive,"University of California, Los Angeles, USA",1,0.92798,,0.07907,,0.7697,,0.5488,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2020-10-16,Adult,Adult,Heart,Cardiovascular System
10058,ERR4691985,ERX4613066,ERS5216072,ERP124560,PRJEB40865,RNA seq of zebrafish adult MCU mutant hearts,ena-STUDY-UCLA-16-10-2020-22:30:44:295-390,Other,We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16,,,zebrafish adult heart RNA,SAMEA7457889,UCLA,ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457889|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 2|common name:zebrafish|dev stage:adult|sample name:wildtype 2|scientific name:Danio rerio|tissue type:heart,,,,,,,,,Illumina HiSeq 3000 sequencing,ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 3000,,ERP124560,Illumina HiSeq 3000 sequencing,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21,WT_2.fastq.gz,fastq,1180831209.0,32069533.0,ena RUN UCLA 16 10 2020 22:30:43:819 2,0:36.82 1:0,A:328604642;C:281065336;G:278743466;T:291039015;N:1378750,36,0,,,328604642,281065336,278743466,291039015,1378750,ERX4613066,ERS5216072,ERA2987364,European Nucleotide Archive,"University of California, Los Angeles, USA",1,0.92319,,0.08946,,0.75706,,0.49996,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2020-10-16,Adult,Adult,Heart,Cardiovascular System
10059,ERR4691984,ERX4613065,ERS5216071,ERP124560,PRJEB40865,RNA seq of zebrafish adult MCU mutant hearts,ena-STUDY-UCLA-16-10-2020-22:30:44:295-390,Other,We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16,,,zebrafish adult heart RNA,SAMEA7457888,UCLA,ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457888|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 1|common name:zebrafish|dev stage:adult|sample name:wildtype 1|scientific name:Danio rerio|tissue type:heart,,,,,,,,,Illumina HiSeq 3000 sequencing,ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 3000,,ERP124560,Illumina HiSeq 3000 sequencing,ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21,WT_1.fastq.gz,fastq,1428414407.0,38793098.0,ena RUN UCLA 16 10 2020 22:30:43:819 1,0:36.82 1:0,A:398925739;C:338731211;G:333527196;T:355553981;N:1676280,36,0,,,398925739,338731211,333527196,355553981,1676280,ERX4613065,ERS5216071,ERA2987364,European Nucleotide Archive,"University of California, Los Angeles, USA",1,0.92407,,0.08758,,0.75726,,0.4969,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2020-10-16,Adult,Adult,Heart,Cardiovascular System
10212,ERR6511331,ERX6138167,ERS7264190,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA,Zebrafish PolyA 4 hpf,SAMEA9541420,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,cDNA8523612,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_polya_4hpf.tar.gz,nanopore,330562220.0,233101.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,0:1418.11,A:86572446;C:74232962;G:69203462;T:100553350;N:0,1418,,,,86572446,74232962,69203462,100553350,0,ERX6138167,ERS7264190,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.0,,0.0,,1.0,,,,1536,,T,,long read,ont,ont,full_length,poly_a,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Blastula,Embryo,Undetermined,Embryo Imprecise
10213,ERR6511329,ERX6138165,ERS7264188,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep1,SAMEA9541418,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541418|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep1|common name:zebrafish|sample name:Zebrafish Ribodep Rep1|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,cDNA786327,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep1.tar.gz,nanopore,1745399583.0,1644167.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,0:1061.57,A:449704009;C:421915878;G:378879857;T:494899839;N:0,1061,,,,449704009,421915878,378879857,494899839,0,ERX6138165,ERS7264188,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.01112,,0.0,,0.99997,,1.0,,546,,T,,long read,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,Embryo,Undetermined,Embryo Imprecise
10215,ERR6511330,ERX6138166,ERS7264189,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep2,SAMEA9541419,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541419|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep2|common name:zebrafish|sample name:Zebrafish Ribodep Rep2|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,cDNA123791,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep2.tar.gz,nanopore,2038398139.0,1955617.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,0:1042.33,A:518369802;C:477535545;G:441294056;T:601198736;N:0,1042,,,,518369802,477535545,441294056,601198736,0,ERX6138166,ERS7264189,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,Embryo,Undetermined,Embryo Imprecise
36581,SRR594769,SRX195432,SRS369361,SRP016134,PRJNA177654,Danio rerio Transcriptome or Gene expression,PRJNA177654,Other,We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.,,,1,Test,GFP Negative 1,,,,,,,,,,,Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development,Embryos,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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>,SRP016134,,,,,2525199228.0,65962848.0,GFP Positive,0:38.28,A:665802914;C:594493287;G:612298433;T:652078696;N:525898,38,,,,665802914,594493287,612298433,652078696,525898,SRX195432,SRS369361,,,University of Cambridge,1,0.89062,,0.09595,,0.74059,,0.47506,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United Kingdom,2015-07-22,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36582,SRR594771,SRX195432,SRS369361,SRP016134,PRJNA177654,Danio rerio Transcriptome or Gene expression,PRJNA177654,Other,We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.,,,1,Test,GFP Negative 1,,,,,,,,,,,Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development,Embryos,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</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>,SRP016134,,,gfp_negative_replicate_1_sequence.txt.gz,fastq,2549682148.0,66546682.0,GFP Negative,0:38.31,A:686329592;C:587342682;G:601330559;T:674194074;N:485241,38,,,,686329592,587342682,601330559,674194074,485241,SRX195432,SRS369361,,,University of Cambridge,1,0.90413,,0.13272,,0.71342,,0.48186,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United Kingdom,2015-07-22,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
36739,SRR867022,SRX286270,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  Bcat,Danio rerio boot,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP022549,,,s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta,SOLiD_native SOLiD_native,9801985250.0,196039705.0,Zebrafish DV patterning Boot,0:50,0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939,50,,,,,,,,,SRX286270,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.59289,,0.09435,,0.92669,,0.7658,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
36740,SRR867023,SRX286271,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  ICH,Danio rerio ICH,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP022549,,,s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual,SOLiD_native SOLiD_native,10810535400.0,216210708.0,Zebrafish DV patterning ICH,0:50,0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417,50,,,,,,,,,SRX286271,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.42474,,0.06136,,0.93434,,0.75757,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
36761,SRR10295266,SRX7008094,SRS431105,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT 2hpf Total mRNA,GSM1152440,,source name:WT 2hpf Total mRNA|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,,,,,,,,,WT 64c R0,AGR000324,AGR000324,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,AGR000324_R1.fastq.gz,fastq,781504124.0,10282949.0,AGR000324 R1.fastq.gz,0:76,A:151879560;C:240178928;G:220957551;T:168456166;N:31919,76,,,,151879560,240178928,220957551,168456166,31919,SRX7008094,SRS431105,SRA980383,Yale_Giraldez|Genetics,"Giraldez Lab, Genetics, Yale University",1,0.88875,,0.14141,,0.796,,0.72154,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2019-10-16,Cleavage,Embryo,Whole Organism,All anatomical structures
37921,SRR1554495,SRX685396,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF4_Ovary_3.fq.gz,fastq,1225610154.0,12134754.0,Ovary2 Run3,0:101,A:347141358;C:303255805;G:280185540;T:294456010;N:571441,101,,,,347141358,303255805,280185540,294456010,571441,SRX685396,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,1e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37922,SRR1554492,SRX685395,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF2_Testis_3.fq.gz,fastq,1192024422.0,11802222.0,Testis2 Run3,0:101,A:373380865;C:276125943;G:251033102;T:290931637;N:552875,101,,,,373380865,276125943,251033102,290931637,552875,SRX685395,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,1e-05,,0.99997,,0.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37923,SRR1554489,SRX685394,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF2_Heart_3.fq.gz,fastq,1302765670.0,12898670.0,Heart2 Run3,0:101,A:397689061;C:312745449;G:268626802;T:323141419;N:562939,101,,,,397689061,312745449,268626802,323141419,562939,SRX685394,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,2e-05,,0.99997,,1.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37924,SRR1554486,SRX685392,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF2_Brain_3.fq.gz,fastq,1211892536.0,11998936.0,Brain2 Run3,0:101,A:374228993;C:286134640;G:253944548;T:297038575;N:545780,101,,,,374228993,286134640,253944548,297038575,545780,SRX685392,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37925,SRR1554483,SRX685391,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF3_Ovary_3.fq.gz,fastq,347516154.0,3440754.0,Ovary1 Run3,0:101,A:107805981;C:80183725;G:73617313;T:85763181;N:145954,101,,,,107805981,80183725,73617313,85763181,145954,SRX685391,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,5e-05,,4e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37926,SRR1554480,SRX685390,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF1_Testis_3.fq.gz,fastq,1184228636.0,11725036.0,Testis1 Run3,0:101,A:340636900;C:278505979;G:259975802;T:304564724;N:545231,101,,,,340636900,278505979,259975802,304564724,545231,SRX685390,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,1e-05,,0.0,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37927,SRR1554477,SRX685389,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF1_Heart_3.fq.gz,fastq,1561371524.0,15459124.0,Heart1 Run3,0:101,A:454757966;C:391143691;G:334715236;T:380114024;N:640607,101,,,,454757966,391143691,334715236,380114024,640607,SRX685389,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,2e-05,,0.99997,,1.0,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37928,SRR1554474,SRX685388,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 2,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP039502,,,ZF1_Brain_3.fq.gz,fastq,1192445794.0,11806394.0,Brain1 Run3,0:101,A:369786121;C:268557682;G:265557417;T:288006805;N:537769,101,,,,369786121,268557682,265557417,288006805,537769,SRX685388,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,1e-05,,1.0,,,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37929,SRR1554493,SRX683354,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF4_Ovary_1.fq.gz,fastq,476104278.0,9335378.0,Ovary2 Run1,0:51,A:111060704;C:120863975;G:129849761;T:114224677;N:105161,51,,,,111060704,120863975,129849761,114224677,105161,SRX683354,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00027,,8e-05,,0.99945,,0.8125,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37930,SRR1554494,SRX683354,SRS686645,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF4Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary2,ZF4Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF4_Ovary_2.fq.gz,fastq,561956352.0,11018752.0,Ovary2 Run2,0:51,A:129925815;C:148479658;G:148478706;T:132824290;N:2247883,51,,,,129925815,148479658,148478706,132824290,2247883,SRX683354,SRS686645,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00022,,0.0001,,0.99967,,0.6875,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37931,SRR1554490,SRX683353,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF2_Testis_1.fq.gz,fastq,586152231.0,11493181.0,Testis2 Run1,0:51,A:145360493;C:148943988;G:151402108;T:140286245;N:159397,51,,,,145360493,148943988,151402108,140286245,159397,SRX683353,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,8e-05,,2e-05,,0.99985,,0.57142,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37932,SRR1554491,SRX683353,SRS686644,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis2,ZF2Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF2_Testis_2.fq.gz,fastq,697016337.0,13666987.0,Testis2 Run2,0:51,A:172082858;C:184634425;G:173370430;T:163527914;N:3400710,51,,,,172082858,184634425,173370430,163527914,3400710,SRX683353,SRS686644,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,8e-05,,2e-05,,0.99985,,0.57142,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37933,SRR1554487,SRX683351,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF2_Heart_1.fq.gz,fastq,767836212.0,15055612.0,Heart2 Run1,0:51,A:192620363;C:202013249;G:191038597;T:181862075;N:301928,51,,,,192620363,202013249,191038597,181862075,301928,SRX683351,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,5e-05,,3e-05,,0.99995,,1.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37934,SRR1554488,SRX683351,SRS686642,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Heart2,ZF2Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF2_Heart_2.fq.gz,fastq,979886205.0,19213455.0,Heart2 Run2,0:51,A:246169086;C:264387065;G:236377487;T:227289693;N:5662874,51,,,,246169086,264387065,236377487,227289693,5662874,SRX683351,SRS686642,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,2e-05,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37935,SRR1554484,SRX683268,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF2_Brain_1.fq.gz,fastq,654412671.0,12831621.0,Brain2 Run1,0:51,A:160544180;C:166355290;G:168608762;T:158684308;N:220131,51,,,,160544180,166355290,168608762,158684308,220131,SRX683268,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,3e-05,,0.0,,0.99993,,1.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37936,SRR1554485,SRX683268,SRS686641,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF2Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain2,ZF2Brain1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF2_Brain_2.fq.gz,fastq,856322793.0,16790643.0,Brain2 Run2,0:51,A:210706815;C:226772546;G:212404752;T:201722093;N:4716587,51,,,,210706815,226772546,212404752,201722093,4716587,SRX683268,SRS686641,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37937,SRR1554481,SRX683080,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF3_Ovary_1.fq.gz,fastq,116086965.0,2276215.0,Ovary1 Run1,0:51,A:29237121;C:30235277;G:29264328;T:27320814;N:29425,51,,,,29237121,30235277,29264328,27320814,29425,SRX683080,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00022,,9e-05,,0.99967,,0.65,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37938,SRR1554482,SRX683080,SRS686559,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF3Ovary1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Ovary1,ZF3Ovary1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF3_Ovary_2.fq.gz,fastq,138905844.0,2723644.0,Ovary1 Run2,0:51,A:34695180;C:38015933;G:33434207;T:32057083;N:703441,51,,,,34695180,38015933,33434207,32057083,703441,SRX683080,SRS686559,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00016,,5e-05,,0.99977,,0.42857,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37939,SRR1554478,SRX683062,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF1_Testis_1.fq.gz,fastq,655515750.0,12853250.0,Testis1 Run1,0:51,A:152422885;C:163771947;G:179144090;T:159997538;N:179290,51,,,,152422885,163771947,179144090,159997538,179290,SRX683062,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0011,,0.00053,,0.99829,,0.67777,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37940,SRR1554479,SRX683062,SRS686542,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Testis1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Testis1,ZF1Testis1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF1_Testis_2.fq.gz,fastq,777594399.0,15246949.0,Testis1 Run2,0:51,A:180116528;C:202508153;G:204833105;T:186435696;N:3700917,51,,,,180116528,202508153,204833105,186435696,3700917,SRX683062,SRS686542,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.00073,,0.00032,,0.99898,,0.62745,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Gonad,Reproductive System
37941,SRR1554475,SRX482035,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF1_Heart_1.fq.gz,fastq,810162642.0,15885542.0,Heart1 Run1,0:51,A:199665102;C:213941735;G:204361738;T:191870055;N:324012,51,,,,199665102,213941735,204361738,191870055,324012,SRX482035,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,6e-05,,1e-05,,0.99989,,0.8,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37942,SRR1554476,SRX482035,SRS566618,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Heart1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish individual 1 heart,ZF1Heart1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF1_Heart_2.fq.gz,fastq,1013563698.0,19873798.0,Heart1 Run2,0:51,A:249913434;C:275453651;G:247166233;T:235034199;N:5996181,51,,,,249913434,275453651,247166233,235034199,5996181,SRX482035,SRS566618,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,4e-05,,2e-05,,0.99997,,0.0,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Heart,Cardiovascular System
37943,SRR1554472,SRX481992,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF1_Brain_1.fq.gz,fastq,679860294.0,13330594.0,Brain1 Run1,0:51,A:167202435;C:176450132;G:174468721;T:161497185;N:241821,51,,,,167202435,176450132,174468721,161497185,241821,SRX481992,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
37944,SRR1554473,SRX481992,SRS566490,SRP039502,PRJNA240316,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA240316,Transcriptome Analysis,Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.,,pubmed:24835514,,,ZF1Brain1,,strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain1,ZFBrain1 1,1,Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.,,,miRNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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>,SRP039502,,,ZF1_Brain_2.fq.gz,fastq,838372782.0,16438682.0,Brain1 Run2,0:51,A:206906228;C:221202670;G:210716690;T:195319694;N:4227500,51,,,,206906228,221202670,210716690,195319694,4227500,SRX481992,SRS566490,SRA142461,University of Oregon|JHP-Lab,University of Oregon,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2014-08-22,Adult,Adult,Brain,Nervous System
39687,SRR2051113,SRX1048368,SRS952733,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P39,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 4,P39,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P39_EL4517_GATCAG_L001_R1_001.fastq.gz P39_EL4517_GATCAG_L002_R1_001.fastq.gz P39_EL4517_GATCAG_L007_R1_001.fastq.gz P39_EL4517_GATCAG_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4090297192.0,40497992.0,P39,0:101,A:1016157993;C:993771683;G:965986507;T:1113686588;N:694421,101,,,,1016157993,993771683,965986507,1113686588,694421,SRX1048368,SRS952733,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9417,,0.14428,,0.68937,,0.5438,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39688,SRR2051110,SRX1048367,SRS952731,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P37,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 3,P37,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P37_EL4516_ACTTGA_L008_R1_001.fastq.gz P37_EL4516_ACTTGA_L007_R1_001.fastq.gz P37_EL4516_ACTTGA_L002_R1_001.fastq.gz P37_EL4516_ACTTGA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4647442886.0,46014286.0,P37,0:101,A:1149955739;C:1129088798;G:1093234722;T:1274375148;N:788479,101,,,,1149955739,1129088798,1093234722,1274375148,788479,SRX1048367,SRS952731,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94585,,0.12571,,0.68633,,0.52597,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39689,SRR2051112,SRX1048366,SRS952732,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P36,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 2,P36,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P36_EL4527_CCGTCC_L008_R1_001.fastq.gz P36_EL4527_CCGTCC_L007_R1_001.fastq.gz P36_EL4527_CCGTCC_L002_R1_001.fastq.gz P36_EL4527_CCGTCC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4296894611.0,42543511.0,P36,0:101,A:1050039699;C:1061123166;G:1022913715;T:1162094624;N:723407,101,,,,1050039699,1061123166,1022913715,1162094624,723407,SRX1048366,SRS952732,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94977,,0.13188,,0.70976,,0.52728,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39690,SRR2051109,SRX1048365,SRS952730,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P35,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 1,P35,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P35_EL4526_ATGTCA_L008_R1_001.fastq.gz P35_EL4526_ATGTCA_L007_R1_001.fastq.gz P35_EL4526_ATGTCA_L002_R1_001.fastq.gz P35_EL4526_ATGTCA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4094752706.0,40542106.0,P35,0:101,A:1009779802;C:1004374749;G:969241794;T:1110655194;N:701167,101,,,,1009779802,1004374749,969241794,1110655194,701167,SRX1048365,SRS952730,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94442,,0.13203,,0.70023,,0.53953,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39691,SRR2051102,SRX1048364,SRS952729,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P29,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 4,P29,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P29_EL4510_CTTGTA_L008_R1_001.fastq.gz P29_EL4510_CTTGTA_L007_R1_001.fastq.gz P29_EL4510_CTTGTA_L002_R1_001.fastq.gz P29_EL4510_CTTGTA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4983571896.0,49342296.0,P29,0:101,A:1247122516;C:1202173111;G:1173654831;T:1359775597;N:845841,101,,,,1247122516,1202173111,1173654831,1359775597,845841,SRX1048364,SRS952729,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94329,,0.13234,,0.68286,,0.51586,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39692,SRR2051100,SRX1048363,SRS952727,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P28,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 3,P28,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P28_EL4509_CAGATC_L008_R1_001.fastq.gz P28_EL4509_CAGATC_L007_R1_001.fastq.gz P28_EL4509_CAGATC_L002_R1_001.fastq.gz P28_EL4509_CAGATC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4032678914.0,39927514.0,P28,0:101,A:1015356577;C:970369004;G:937306142;T:1108957703;N:689488,101,,,,1015356577,970369004,937306142,1108957703,689488,SRX1048363,SRS952727,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93887,,0.13869,,0.69079,,0.52237,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39693,SRR2051101,SRX1048362,SRS952728,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P26,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 2,P26,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P26_EL4508_GCCAAT_L001_R1_001.fastq.gz P26_EL4508_GCCAAT_L007_R1_001.fastq.gz P26_EL4508_GCCAAT_L008_R1_001.fastq.gz P26_EL4508_GCCAAT_L002_R1_001.fastq.gz,fastq fastq fastq fastq,6526758875.0,64621375.0,P26,0:101,A:1635664768;C:1568967965;G:1518148006;T:1802863908;N:1114228,101,,,,1635664768,1568967965,1518148006,1802863908,1114228,SRX1048362,SRS952728,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93822,,0.15203,,0.68609,,0.53171,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39694,SRR2051096,SRX1048361,SRS952726,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P25,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 1,P25,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P25_EL4511_ATCACG_L001_R1_001.fastq.gz P25_EL4511_ATCACG_L002_R1_001.fastq.gz P25_EL4511_ATCACG_L007_R1_001.fastq.gz P25_EL4511_ATCACG_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4185957322.0,41445122.0,P25,0:101,A:1081936223;C:978799105;G:956795307;T:1167714259;N:712428,101,,,,1081936223,978799105,956795307,1167714259,712428,SRX1048361,SRS952726,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9288,,0.17032,,0.6801,,0.51298,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39695,SRR2051095,SRX1048360,SRS952725,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P19,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 4,P19,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P19_EL4521_GGCTAC_L008_R1_001.fastq.gz P19_EL4521_GGCTAC_L007_R1_001.fastq.gz P19_EL4521_GGCTAC_L002_R1_001.fastq.gz P19_EL4521_GGCTAC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4293546461.0,42510361.0,P19,0:101,A:1062707728;C:1045602693;G:1011860446;T:1172670772;N:704822,101,,,,1062707728,1045602693,1011860446,1172670772,704822,SRX1048360,SRS952725,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94381,,0.13697,,0.69051,,0.51415,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39696,SRR2051094,SRX1048359,SRS952724,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P18,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 3,P18,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P18_EL4520_TAGCTT_L008_R1_001.fastq.gz P18_EL4520_TAGCTT_L007_R1_001.fastq.gz P18_EL4520_TAGCTT_L002_R1_001.fastq.gz P18_EL4520_TAGCTT_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4257944163.0,42157863.0,P18,0:101,A:1044532409;C:1049992329;G:1010166097;T:1152524203;N:729125,101,,,,1044532409,1049992329,1010166097,1152524203,729125,SRX1048359,SRS952724,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94262,,0.14592,,0.69014,,0.52498,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39697,SRR2051093,SRX1048358,SRS952723,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P17,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 2,P17,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P17_EL4522_AGTCAA_L007_R1_001.fastq.gz P17_EL4522_AGTCAA_L008_R1_001.fastq.gz P17_EL4522_AGTCAA_L002_R1_001.fastq.gz P17_EL4522_AGTCAA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4278385553.0,42360253.0,P17,0:101,A:1040955882;C:1060023973;G:1019487833;T:1157186726;N:731139,101,,,,1040955882,1060023973,1019487833,1157186726,731139,SRX1048358,SRS952723,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94697,,0.14458,,0.69643,,0.53451,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39698,SRR2051092,SRX1048357,SRS952722,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P15,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 1,P15,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,P15_EL4523_AGTTCC_L001_R1_001.fastq.gz P15_EL4523_AGTTCC_L002_R1_001.fastq.gz P15_EL4523_AGTTCC_L007_R1_001.fastq.gz P15_EL4523_AGTTCC_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4341747499.0,42987599.0,P15,0:101,A:1052621077;C:1088380866;G:1041958433;T:1158051746;N:735377,101,,,,1052621077,1088380866,1041958433,1158051746,735377,SRX1048357,SRS952722,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94563,,0.153,,0.69822,,0.54133,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39699,SRR2051091,SRX1048356,SRS952721,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN9,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 4,CN9,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,CN9_EL4515_TTAGGC_L001_R1_001.fastq.gz CN9_EL4515_TTAGGC_L002_R1_001.fastq.gz CN9_EL4515_TTAGGC_L007_R1_001.fastq.gz CN9_EL4515_TTAGGC_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4220387212.0,41786012.0,CN9,0:101,A:1031722430;C:1044497851;G:1005706674;T:1137783022;N:677235,101,,,,1031722430,1044497851,1005706674,1137783022,677235,SRX1048356,SRS952721,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.95231,,0.14084,,0.69682,,0.52966,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39700,SRR2051090,SRX1048354,SRS952719,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN8,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 3,CN8,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,CN8_EL4505_CGATGT_L008_R1_001.fastq.gz CN8_EL4505_CGATGT_L007_R1_001.fastq.gz CN8_EL4505_CGATGT_L002_R1_001.fastq.gz CN8_EL4505_CGATGT_L001_R1_001.fastq.gz,fastq fastq fastq fastq,5835502553.0,57777253.0,CN8,0:101,A:1424369529;C:1441755207;G:1391851806;T:1576540272;N:985739,101,,,,1424369529,1441755207,1391851806,1576540272,985739,SRX1048354,SRS952719,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94643,,0.12925,,0.70725,,0.52949,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39701,SRR2050894,SRX1048353,SRS952718,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN7,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 2,CN7,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,CN7_EL4507_ACAGTG_L008_R1_001.fastq.gz CN7_EL4507_ACAGTG_L007_R1_001.fastq.gz CN7_EL4507_ACAGTG_L002_R1_001.fastq.gz CN7_EL4507_ACAGTG_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4789094477.0,47416777.0,CN7,0:101,A:1160528098;C:1197558725;G:1155573375;T:1274638263;N:796016,101,,,,1160528098,1197558725,1155573375,1274638263,796016,SRX1048353,SRS952718,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9501,,0.14828,,0.69966,,0.52764,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39702,SRR2050892,SRX1048352,SRS952717,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN5,,breed:wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 1,CN5,CN5 EL4506 TGACCA,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>,SRP059060,,,CN5_EL4506_TGACCA_L001_R1_001.fastq.gz CN5_EL4506_TGACCA_L002_R1_001.fastq.gz CN5_EL4506_TGACCA_L007_R1_001.fastq.gz CN5_EL4506_TGACCA_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4526144512.0,44813312.0,CN5,0:101,A:1109966549;C:1116619353;G:1075422479;T:1223366972;N:769159,101,,,,1109966549,1116619353,1075422479,1223366972,769159,SRX1048352,SRS952717,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94604,,0.14084,,0.69004,,0.53407,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
41827,SRR5251446,SRX2557171,SRS1974564,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B1,nicoli mutmir AG01645,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B1,AG01645.1,AG01645.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01645.1_R1.fastq.gz,fastq,1574284140.0,20714265.0,AG01645.1 R1.fastq.gz,0:76,A:485471345;C:270854124;G:374164721;T:443766613;N:27337,76,,,,485471345,270854124,374164721,443766613,27337,SRX2557171,SRS1974564,SRA537606,Yale University|Genetics,Yale University,1,0.82142,,0.14068,,0.8002,,0.5444,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-27,Undetermined,Embryo,Endothelium,Cardiovascular System
41828,SRR5251445,SRX2557170,SRS1974563,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B2,nicoli mutmir AG01646,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B2,AG01646.1,AG01646.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01646.1_R1.fastq.gz,fastq,1484740104.0,19536054.0,AG01646.1 R1.fastq.gz,0:76,A:453388316;C:246477203;G:365031959;T:419816346;N:26280,76,,,,453388316,246477203,365031959,419816346,26280,SRX2557170,SRS1974563,SRA537606,Yale University|Genetics,Yale University,1,0.82649,,0.1897,,0.79862,,0.52759,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41829,SRR5251444,SRX2557169,SRS1974562,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B3,nicoli mutmir AG01647,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B3,AG01647.1,AG01647.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01647.1_R1.fastq.gz,fastq,881298660.0,11596035.0,AG01647.1 R1.fastq.gz,0:76,A:270675838;C:160127586;G:228157662;T:222301246;N:36328,76,,,,270675838,160127586,228157662,222301246,36328,SRX2557169,SRS1974562,SRA537606,Yale University|Genetics,Yale University,1,0.76133,,0.15034,,0.83341,,0.56596,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41830,SRR5251443,SRX2557168,SRS1974561,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B1,nicoli mutmir AG01648,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B1,AG01648.1,AG01648.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01648.1_R1.fastq.gz,fastq,637896880.0,8393380.0,AG01648.1 R1.fastq.gz,0:76,A:192829278;C:112701153;G:153321271;T:179019095;N:26083,76,,,,192829278,112701153,153321271,179019095,26083,SRX2557168,SRS1974561,SRA537606,Yale University|Genetics,Yale University,1,0.75971,,0.1181,,0.82171,,0.56797,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41831,SRR5251442,SRX2557167,SRS1974560,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B2,nicoli mutmir AG01649,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B2,AG01649.1,AG01649.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01649.1_R1.fastq.gz,fastq,849868328.0,11182478.0,AG01649.1 R1.fastq.gz,0:76,A:258225905;C:148467172;G:205165181;T:237974100;N:35970,76,,,,258225905,148467172,205165181,237974100,35970,SRX2557167,SRS1974560,SRA537606,Yale University|Genetics,Yale University,1,0.75096,,0.14506,,0.81507,,0.5545,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41832,SRR5251441,SRX2557166,SRS1974559,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B3,nicoli mutmir AG01650,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B3,AG01650.1,AG01650.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01650.1_R1.fastq.gz,fastq,998464668.0,13137693.0,AG01650.1 R1.fastq.gz,0:76,A:311526420;C:176545041;G:251852786;T:258497630;N:42791,76,,,,311526420,176545041,251852786,258497630,42791,SRX2557166,SRS1974559,SRA537606,Yale University|Genetics,Yale University,1,0.76479,,0.11192,,0.82674,,0.54621,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41833,SRR5251440,SRX2557165,SRS1974558,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B1,nicoli mutmir AG01651,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B1,AG01651.1,AG01651.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01651.1_R1.fastq.gz,fastq,570492252.0,7506477.0,AG01651.1 R1.fastq.gz,0:76,A:162512811;C:104071716;G:135730697;T:168149427;N:27601,76,,,,162512811,104071716,135730697,168149427,27601,SRX2557165,SRS1974558,SRA537606,Yale University|Genetics,Yale University,1,0.73988,,0.10157,,0.86647,,0.54252,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41834,SRR5251439,SRX2557164,SRS1974557,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B2,nicoli mutmir AG01652,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B2,AG01652.1,AG01652.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01652.1_R1.fastq.gz,fastq,1072886148.0,14116923.0,AG01652.1 R1.fastq.gz,0:76,A:338399596;C:192703439;G:242960887;T:298769761;N:52465,76,,,,338399596,192703439,242960887,298769761,52465,SRX2557164,SRS1974557,SRA537606,Yale University|Genetics,Yale University,1,0.76456,,0.11024,,0.89197,,0.59214,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41835,SRR5251438,SRX2557163,SRS1974556,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B3,nicoli mutmir AG01653,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B3,AG01653.1,AG01653.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01653.1_R1.fastq.gz,fastq,1016374144.0,13373344.0,AG01653.1 R1.fastq.gz,0:76,A:310958343;C:168702106;G:223420046;T:313241363;N:52286,76,,,,310958343,168702106,223420046,313241363,52286,SRX2557163,SRS1974556,SRA537606,Yale University|Genetics,Yale University,1,0.75735,,0.12224,,0.79756,,0.55136,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41836,SRR5251437,SRX2557162,SRS1974555,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B1,nicoli mutmir AG01654,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B1,AG01654.1,AG01654.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01654.1_R1.fastq.gz,fastq,782170112.0,10291712.0,AG01654.1 R1.fastq.gz,0:76,A:238316720;C:132163709;G:179301544;T:232350598;N:37541,76,,,,238316720,132163709,179301544,232350598,37541,SRX2557162,SRS1974555,SRA537606,Yale University|Genetics,Yale University,1,0.7683,,0.10712,,0.80034,,0.55804,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41837,SRR5251436,SRX2557161,SRS1974554,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B2,nicoli mutmir AG01655,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B2,AG01655.1,AG01655.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01655.1_R1.fastq.gz,fastq,1053946340.0,13867715.0,AG01655.1 R1.fastq.gz,0:76,A:318351311;C:191163031;G:240348413;T:304030367;N:53218,76,,,,318351311,191163031,240348413,304030367,53218,SRX2557161,SRS1974554,SRA537606,Yale University|Genetics,Yale University,1,0.77588,,0.07983,,0.83934,,0.56228,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41838,SRR5251435,SRX2557160,SRS1974553,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B3,nicoli mutmir AG01656,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B3,AG01656.1,AG01656.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01656.1_R1.fastq.gz,fastq,1182467736.0,15558786.0,AG01656.1 R1.fastq.gz,0:76,A:344465226;C:204677242;G:269228338;T:364036735;N:60195,76,,,,344465226,204677242,269228338,364036735,60195,SRX2557160,SRS1974553,SRA537606,Yale University|Genetics,Yale University,1,0.78956,,0.13495,,0.81517,,0.56342,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41839,SRR5251434,SRX2557159,SRS1974552,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B1,nicoli mutmir AG01657,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B1,AG01657.1,AG01657.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01657.1_R1.fastq.gz,fastq,536336712.0,7057062.0,AG01657.1 R1.fastq.gz,0:76,A:158301607;C:93070120;G:121382262;T:163555487;N:27236,76,,,,158301607,93070120,121382262,163555487,27236,SRX2557159,SRS1974552,SRA537606,Yale University|Genetics,Yale University,1,0.76425,,0.1278,,0.84222,,0.55305,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41840,SRR5251433,SRX2557158,SRS1974551,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B2,nicoli mutmir AG01658,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B2,AG01658.1,AG01658.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01658.1_R1.fastq.gz,fastq,798581856.0,10507656.0,AG01658.1 R1.fastq.gz,0:76,A:241352089;C:134327379;G:183394123;T:239469845;N:38420,76,,,,241352089,134327379,183394123,239469845,38420,SRX2557158,SRS1974551,SRA537606,Yale University|Genetics,Yale University,1,0.76221,,0.13398,,0.82459,,0.55228,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41841,SRR5251432,SRX2557157,SRS1974550,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B3,nicoli mutmir AG01659,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B3,AG01659.1,AG01659.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01659.1_R1.fastq.gz,fastq,1093998948.0,14394723.0,AG01659.1 R1.fastq.gz,0:76,A:330741822;C:186325335;G:249557623;T:327320449;N:53719,76,,,,330741822,186325335,249557623,327320449,53719,SRX2557157,SRS1974550,SRA537606,Yale University|Genetics,Yale University,1,0.77108,,0.14674,,0.80955,,0.55819,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41842,SRR5251431,SRX2557156,SRS1974549,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR223 B1,nicoli mutmir AG01660,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR223 B1,AG01660.1,AG01660.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01660.1_R1.fastq.gz,fastq,849905492.0,11182967.0,AG01660.1 R1.fastq.gz,0:76,A:250953875;C:146191904;G:190040699;T:262674911;N:44103,76,,,,250953875,146191904,190040699,262674911,44103,SRX2557156,SRS1974549,SRA537606,Yale University|Genetics,Yale University,1,0.7687,,0.14192,,0.82842,,0.5344,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41843,SRR5251430,SRX2557155,SRS1974548,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR223 B2,nicoli mutmir AG01661,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR223 B2,AG01661.1,AG01661.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01661.1_R1.fastq.gz,fastq,840115400.0,11054150.0,AG01661.1 R1.fastq.gz,0:76,A:257057495;C:141775085;G:188281166;T:252960590;N:41064,76,,,,257057495,141775085,188281166,252960590,41064,SRX2557155,SRS1974548,SRA537606,Yale University|Genetics,Yale University,1,0.74292,,0.10759,,0.83615,,0.55136,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
43058,SRR8354695,SRX5165478,SRS4174524,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS seq   RNA structure positive controls in vitro replicate 1,DMS seq   RNA positives ctrl in vitro B1 AG01489,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,DMS seq   RNA structure positive controls in vitro replicate 1,AG01489.1,AG01489.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,AG01489.1_R1.fastq.gz,fastq,75703530.0,2718404.0,AG01489.1 R1.fastq.gz,0:27.85 1:0,A:18206335;C:19464567;G:21319876;T:16712584;N:168,27,0,,,18206335,19464567,21319876,16712584,168,SRX5165478,SRS4174524,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.02389,,0.00591,,0.97654,,0.4758,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43059,SRR8354696,SRX5165477,SRS4174523,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS seq   RNA structure positive controls in vitro replicate 2,DMS seq   RNA positives ctrl in vitro B2 AG01490,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,DMS seq   RNA structure positive controls in vitro replicate 2,AG01490.1,AG01490.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,AG01490.1_R1.fastq.gz,fastq,295051199.0,10869746.0,AG01490.1 R1.fastq.gz,0:27.14 1:0,A:71900468;C:76519029;G:81589099;T:65042019;N:584,27,0,,,71900468,76519029,81589099,65042019,584,SRX5165477,SRS4174523,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.02362,,0.00528,,0.98173,,0.35096,,19,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43060,SRR8354697,SRX5165476,SRS4174522,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2,Raw multiplex: DMS seq   RNA positives ctrl in vitro B1 AG01489;DMS seq   RNA positives ctrl in vitro B2 AG01490,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1;2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2,AG01489.1;AG01490.1,AG01489.1;AG01490.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MYYANXX_JBDX127_009_R1.fastq.gz,fastq,1115150128.0,14673028.0,C7MYYANXX JBDX127 009 R1.fastq.gz,0:76,A:313482382;C:276309346;G:291633361;T:233659719;N:65320,76,,,,313482382,276309346,291633361,233659719,65320,SRX5165476,SRS4174522,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00546,,0.00047,,0.98602,,0.51535,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43061,SRR7264565,SRX4168732,SRS3380685,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated,,strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,AG01046.2;AG01047.2;AG01049.2;unrelated,AG01046.2;AG01047.2;AG01049.2;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HA22NADXX_JBBS71_021_R1.fastq.gz,fastq,493969676.0,6499601.0,HA22NADXX JBBS71 021 R1.fastq.gz,0:76,A:149523181;C:122615352;G:117180131;T:97949905;N:6701107,76,,,,149523181,122615352,117180131,97949905,6701107,SRX4168732,SRS3380685,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43062,SRR7264566,SRX4168731,SRS3380685,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated,,strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,AG01046.1;AG01047.1;AG01049.1;unrelated,AG01046.1;AG01047.1;AG01049.1;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HA1YWADXX_JBBS71_021_R1.fastq.gz,fastq,1444702012.0,19009237.0,HA1YWADXX JBBS71 021 R1.fastq.gz,0:76,A:442549747;C:365473385;G:344546726;T:292070542;N:61612,76,,,,442549747,365473385,344546726,292070542,61612,SRX4168731,SRS3380685,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43063,SRR7264567,SRX4168730,SRS3380690,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated,,strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,AG01042.6;AG01043.6;AG01044.6;unrelated,AG01042.6;AG01043.6;AG01044.6;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HBCAFADXX_JBBR70_020_R1.fastq.gz,fastq,3562176468.0,46870743.0,HBCAFADXX JBBR70 020 R1.fastq.gz,0:76,A:1097921080;C:906895047;G:849908073;T:707369464;N:82804,76,,,,1097921080,906895047,849908073,707369464,82804,SRX4168730,SRS3380690,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43064,SRR7264568,SRX4168729,SRS3380690,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated,,strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,AG01042.5;AG01043.5;AG01044.5;unrelated,AG01042.5;AG01043.5;AG01044.5;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,C562AACXX_JBBR70_NOBCX_R1.fastq.gz,fastq,13352386192.0,175689292.0,C562AACXX JBBR70 NOBCX R1.fastq.gz,0:76,A:4126007145;C:3372127203;G:3172182791;T:2661287884;N:20781169,76,,,,4126007145,3372127203,3172182791,2661287884,20781169,SRX4168729,SRS3380690,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43065,SRR7264569,SRX4168728,SRS3380690,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated,,strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,AG01042.4;AG01043.4;AG01044.4;unrelated,AG01042.4;AG01043.4;AG01044.4;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HA2H1ADXX_JBBR70_NOBCX_R1.fastq.gz,fastq,9139389880.0,120255130.0,HA2H1ADXX JBBR70 NOBCX R1.fastq.gz,0:76,A:2815354570;C:2322972018;G:2180978488;T:1817457488;N:2627316,76,,,,2815354570,2322972018,2180978488,1817457488,2627316,SRX4168728,SRS3380690,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43066,SRR7264570,SRX4168727,SRS3380690,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated,,strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,AG01042.3;AG01043.3;AG01044.3;unrelated,AG01042.3;AG01043.3;AG01044.3;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HA1YVADXX_JBBR70_NOBCX_R1.fastq.gz,fastq,7892000132.0,103842107.0,HA1YVADXX JBBR70 NOBCX R1.fastq.gz,0:76,A:2428266964;C:2007082407;G:1885147455;T:1568726692;N:2776614,76,,,,2428266964,2007082407,1885147455,1568726692,2776614,SRX4168727,SRS3380690,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43067,SRR7264571,SRX4168726,SRS3380690,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated,,strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,AG01042.2;AG01043.2;AG01044.2;unrelated,AG01042.2;AG01043.2;AG01044.2;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HA22NADXX_JBBR70_020_R1.fastq.gz,fastq,554569568.0,7296968.0,HA22NADXX JBBR70 020 R1.fastq.gz,0:76,A:168630291;C:138451887;G:131779810;T:108186590;N:7520990,76,,,,168630291,138451887,131779810,108186590,7520990,SRX4168726,SRS3380690,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43068,SRR7264572,SRX4168725,SRS3380690,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated,,strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated,AG01042.1;AG01043.1;AG01044.1;unrelated,AG01042.1;AG01043.1;AG01044.1;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HA1YWADXX_JBBR70_020_R1.fastq.gz,fastq,1565371316.0,20596991.0,HA1YWADXX JBBR70 020 R1.fastq.gz,0:76,A:481887814;C:398331513;G:374271346;T:310815367;N:65276,76,,,,481887814,398331513,374271346,310815367,65276,SRX4168725,SRS3380690,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43069,SRR7264573,SRX4168724,SRS3380685,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated,,strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,AG01046.4;AG01047.4;AG01049.4;unrelated,AG01046.4;AG01047.4;AG01049.4;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HA2H1ADXX_JBBS71_NOBCX_R1.fastq.gz,fastq,8845878184.0,116393134.0,HA2H1ADXX JBBS71 NOBCX R1.fastq.gz,0:76,A:2711637569;C:2235324807;G:2105535243;T:1791610098;N:1770467,76,,,,2711637569,2235324807,2105535243,1791610098,1770467,SRX4168724,SRS3380685,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43070,SRR7264574,SRX4168723,SRS3380685,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated,,strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,AG01046.3;AG01047.3;AG01049.3;unrelated,AG01046.3;AG01047.3;AG01049.3;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HA1YVADXX_JBBS71_NOBCX_R1.fastq.gz,fastq,7768733452.0,102220177.0,HA1YVADXX JBBS71 NOBCX R1.fastq.gz,0:76,A:2378019627;C:1963788516;G:1851111018;T:1572409542;N:3404749,76,,,,2378019627,1963788516,1851111018,1572409542,3404749,SRX4168723,SRS3380685,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,1e-05,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43071,SRR7264575,SRX4168722,SRS3380686,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2,Raw multiplex: dmsseq AG01273;dmsseq AG01274,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2,AG01273.4;AG01274.4,AG01273.4;AG01274.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HWKVWADXX_JBCZ103_023_R1.fastq.gz,fastq,7514617040.0,98876540.0,HWKVWADXX JBCZ103 023 R1.fastq.gz,0:76,A:2401597632;C:1861527917;G:1834777254;T:1415956870;N:757367,76,,,,2401597632,1861527917,1834777254,1415956870,757367,SRX4168722,SRS3380686,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43072,SRR7264576,SRX4168721,SRS3380689,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: RPF patA   WT 64c RPF B1;RPF patA   WT 64c RPF B2,Raw multiplex: ribo seq pata AG01409;ribo seq pata AG01410,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex|molecule:RNA|condition:RPF 28nt|replicate group:19|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: RPF patA   WT 64c RPF B1;RPF patA   WT 64c RPF B2,AG01409.1;AG01410.1,AG01409.1;AG01410.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MPPANXX_JBDL115_014_R1.fastq.gz,fastq,4944760108.0,65062633.0,C7MPPANXX JBDL115 014 R1.fastq.gz,0:76,A:1280812305;C:1385761238;G:1441128504;T:836702863;N:355198,76,,,,1280812305,1385761238,1441128504,836702863,355198,SRX4168721,SRS3380689,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43073,SRR7264577,SRX4168720,SRS3380688,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: RPF patA   WT 64c PatA RPF B1;RPF patA   WT 64c PatA RPF B2,Raw multiplex: ribo seq pata AG01411;ribo seq pata AG01412,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex PatA|molecule:RNA|condition:RPF 28nt|replicate group:20|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: RPF patA   WT 64c PatA RPF B1;RPF patA   WT 64c PatA RPF B2,AG01411.1;AG01412.1,AG01411.1;AG01412.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MPPANXX_JBDM116_015_R1.fastq.gz,fastq,10995071544.0,144671994.0,C7MPPANXX JBDM116 015 R1.fastq.gz,0:76,A:2850888928;C:3075001734;G:3215965099;T:1852417694;N:798089,76,,,,2850888928,3075001734,3215965099,1852417694,798089,SRX4168720,SRS3380688,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43074,SRR7264578,SRX4168719,SRS3380687,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2,Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2,AG01426.1;AG01427.1,AG01426.1;AG01427.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MPPANXX_JBDF109_027_R1.fastq.gz,fastq,446991948.0,5881473.0,C7MPPANXX JBDF109 027 R1.fastq.gz,0:76,A:146192524;C:109441919;G:103882304;T:87445288;N:29913,76,,,,146192524,109441919,103882304,87445288,29913,SRX4168719,SRS3380687,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,2e-05,,1e-05,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43075,SRR7264579,SRX4168718,SRS3380687,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2,Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2,AG01426.2;AG01427.2,AG01426.2;AG01427.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HVJC2ADXX_JBDF109_027_R1.fastq.gz,fastq,447485492.0,5887967.0,HVJC2ADXX JBDF109 027 R1.fastq.gz,0:76,A:146683880;C:109166579;G:104154702;T:87473352;N:6979,76,,,,146683880,109166579,104154702,87473352,6979,SRX4168718,SRS3380687,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0023,,0.00034,,0.99326,,0.57567,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43076,SRR7264580,SRX4168717,SRS3380687,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2,Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2,AG01426.3;AG01427.3,AG01426.3;AG01427.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HVJ2TADXX_JBDF109_027_R1.fastq.gz,fastq,4740289176.0,62372226.0,HVJ2TADXX JBDF109 027 R1.fastq.gz,0:76,A:1552060471;C:1156267615;G:1104246757;T:927209997;N:504336,76,,,,1552060471,1156267615,1104246757,927209997,504336,SRX4168717,SRS3380687,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00235,,0.00026,,0.99379,,0.60051,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43077,SRR7264581,SRX4168716,SRS3380687,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2,Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2,AG01426.4;AG01427.4,AG01426.4;AG01427.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HJTYNBCXX_JBDF109_NOBCX_R1.fastq.gz,fastq,6776423036.0,89163461.0,HJTYNBCXX JBDF109 NOBCX R1.fastq.gz,0:76,A:2212424663;C:1653496002;G:1573846163;T:1336100302;N:555906,76,,,,2212424663,1653496002,1573846163,1336100302,555906,SRX4168716,SRS3380687,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,3e-05,,2e-05,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43078,SRR7264582,SRX4168715,SRS3380683,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2,Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2,AG01428.1;AG01429.1,AG01428.1;AG01429.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MPPANXX_JBDG110_013_R1.fastq.gz,fastq,1593732388.0,20970163.0,C7MPPANXX JBDG110 013 R1.fastq.gz,0:76,A:517196379;C:393268952;G:372639155;T:310521534;N:106368,76,,,,517196379,393268952,372639155,310521534,106368,SRX4168715,SRS3380683,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,2e-05,,0.0,,0.99997,,1.0,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43079,SRR7264583,SRX4168714,SRS3380683,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2,Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2,AG01428.2;AG01429.2,AG01428.2;AG01429.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HVJC2ADXX_JBDG110_013_R1.fastq.gz,fastq,1268326988.0,16688513.0,HVJC2ADXX JBDG110 013 R1.fastq.gz,0:76,A:411772190;C:312434121;G:297408612;T:246654231;N:57834,76,,,,411772190,312434121,297408612,246654231,57834,SRX4168714,SRS3380683,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,1e-05,,0.0,,0.99997,,0.0,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43080,SRR7264584,SRX4168713,SRS3380683,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2,Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2,AG01428.3;AG01429.3,AG01428.3;AG01429.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HVJ2TADXX_JBDG110_013_R1.fastq.gz,fastq,1149592188.0,15126213.0,HVJ2TADXX JBDG110 013 R1.fastq.gz,0:76,A:373090462;C:283151050;G:269811169;T:223419849;N:119658,76,,,,373090462,283151050,269811169,223419849,119658,SRX4168713,SRS3380683,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00222,,0.0002,,0.99362,,0.55643,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43081,SRR7264585,SRX4168712,SRS3380686,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2,Raw multiplex: dmsseq AG01273;dmsseq AG01274,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2,AG01273.3;AG01274.3,AG01273.3;AG01274.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HVJ7NADXX_JBCZ103_023_R1.fastq.gz,fastq,882016024.0,11605474.0,HVJ7NADXX JBCZ103 023 R1.fastq.gz,0:76,A:278837606;C:213606139;G:214029888;T:175477675;N:64716,76,,,,278837606,213606139,214029888,175477675,64716,SRX4168712,SRS3380686,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,6e-05,,4e-05,,0.99995,,1.0,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43082,SRR7264586,SRX4168711,SRS3380686,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2,Raw multiplex: dmsseq AG01273;dmsseq AG01274,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2,AG01273.2;AG01274.2,AG01273.2;AG01274.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HVK53ADXX_JBCZ103_023_R1.fastq.gz,fastq,2614864056.0,34406106.0,HVK53ADXX JBCZ103 023 R1.fastq.gz,0:76,A:832670351;C:647746556;G:639758530;T:494461931;N:226688,76,,,,832670351,647746556,639758530,494461931,226688,SRX4168711,SRS3380686,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,5e-05,,2e-05,,0.99993,,0.0,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43083,SRR7264587,SRX4168710,SRS3380684,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1,Raw multiplex: dmsseq AG01269;dmsseq AG01270,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1,AG01269.4;AG01270.4,AG01269.4;AG01270.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MYYANXX_JBCX101_016_R1.fastq.gz,fastq,3504515800.0,46112050.0,C7MYYANXX JBCX101 016 R1.fastq.gz,0:76,A:1100987855;C:897481291;G:850509260;T:655386223;N:151171,76,,,,1100987855,897481291,850509260,655386223,151171,SRX4168710,SRS3380684,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00251,,0.00024,,0.99334,,0.49363,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-05,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
43084,SRR7264588,SRX4168709,SRS3380684,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1,Raw multiplex: dmsseq AG01269;dmsseq AG01270,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1,AG01269.3;AG01270.3,AG01269.3;AG01270.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HVJ7NADXX_JBCX101_016_R1.fastq.gz,fastq,1533760484.0,20181059.0,HVJ7NADXX JBCX101 016 R1.fastq.gz,0:76,A:486730101;C:387546602;G:372319444;T:287072948;N:91389,76,,,,486730101,387546602,372319444,287072948,91389,SRX4168709,SRS3380684,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,4e-05,,2e-05,,0.99997,,1.0,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
43085,SRR7264589,SRX4168708,SRS3380686,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2,Raw multiplex: dmsseq AG01273;dmsseq AG01274,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2,AG01273.1;AG01274.1,AG01273.1;AG01274.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,HMHGVADXX_JBCZ103_023_R1.fastq.gz,fastq,2819768568.0,37102218.0,HMHGVADXX JBCZ103 023 R1.fastq.gz,0:76,A:900945260;C:699348182;G:689446355;T:529699985;N:328786,76,,,,900945260,699348182,689446355,529699985,328786,SRX4168708,SRS3380686,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
43086,SRR7264590,SRX4168707,SRS3380684,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1,Raw multiplex: dmsseq AG01269;dmsseq AG01270,,strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1,AG01269.5;AG01270.5,AG01269.5;AG01270.5,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MWLANXX_JBCX101_016_R1.fastq.gz,fastq,11187105076.0,147198751.0,C7MWLANXX JBCX101 016 R1.fastq.gz,0:76,A:3525623658;C:2869684594;G:2708534500;T:2083102664;N:159660,76,,,,3525623658,2869684594,2708534500,2083102664,159660,SRX4168707,SRS3380684,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
43087,SRR7264591,SRX4168706,SRS3380685,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated,,strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,AG01046.6;AG01047.6;AG01049.6;unrelated,AG01046.6;AG01047.6;AG01049.6;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,HBCAFADXX_JBBS71_021_R1.fastq.gz,fastq,5103002976.0,67144776.0,HBCAFADXX JBBS71 021 R1.fastq.gz,0:76,A:1565087315;C:1292145008;G:1214936605;T:1030712352;N:121696,76,,,,1565087315,1292145008,1214936605,1030712352,121696,SRX4168706,SRS3380685,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,2e-05,,1e-05,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
43088,SRR7264592,SRX4168705,SRS3380685,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated,,strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated,AG01046.5;AG01047.5;AG01049.5;unrelated,AG01046.5;AG01047.5;AG01049.5;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,C562AACXX_JBBS71_NOBCX_R1.fastq.gz,fastq,11245730944.0,147970144.0,C562AACXX JBBS71 NOBCX R1.fastq.gz,0:76,A:3451642355;C:2826476753;G:2670179644;T:2277897894;N:19534298,76,,,,3451642355,2826476753,2670179644,2277897894,19534298,SRX4168705,SRS3380685,SRA715414,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures