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
9361,ERR3011947,ERX3014407,ERS2994081,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Flutamide 2,SAMEA5186582,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186582|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 2|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:Flutamide 2 s,Flutamide 2 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:flutamide|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_Flutamide_2_R1.fastq.gz,fastq,1754963940.0,23552243.0,E MTAB 7283:Flutamide 2,0:74.51 1:0,A:455444321;C:410713896;G:385640226;T:503155736;N:9761,74,0,,,455444321,410713896,385640226,503155736,9761,ERX3014407,ERS2994081,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94351,,0.11595,,0.67483,,0.48762,,73,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9362,ERR3011946,ERX3014406,ERS2994080,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Flutamide 1,SAMEA5186581,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186581|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 1|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:Flutamide 1 s,Flutamide 1 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:flutamide|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_Flutamide_1_R1.fastq.gz,fastq,1631102863.0,21898245.0,E MTAB 7283:Flutamide 1,0:74.49 1:0,A:424378341;C:380806325;G:358128992;T:467779945;N:9260,74,0,,,424378341,380806325,358128992,467779945,9260,ERX3014406,ERS2994080,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94332,,0.11797,,0.67596,,0.48847,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9363,ERR3011945,ERX3014405,ERS2994079,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,DMSO 2,SAMEA5186580,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186580|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 2|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:DMSO 2 s,DMSO 2 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_DMSO_2_R1.fastq.gz,fastq,1811573293.0,24316929.0,E MTAB 7283:DMSO 2,0:74.50 1:0,A:470888315;C:423635861;G:396796840;T:520242179;N:10098,74,0,,,470888315,423635861,396796840,520242179,10098,ERX3014405,ERS2994079,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94219,,0.12305,,0.67184,,0.47704,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9364,ERR3011944,ERX3014404,ERS2994078,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,DMSO 1,SAMEA5186579,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186579|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 1|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:DMSO 1 s,DMSO 1 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_DMSO_1_R1.fastq.gz,fastq,1609807409.0,21611475.0,E MTAB 7283:DMSO 1,0:74.49 1:0,A:420253680;C:374436301;G:352526427;T:462581933;N:9068,74,0,,,420253680,374436301,352526427,462581933,9068,ERX3014404,ERS2994078,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94094,,0.12292,,0.67006,,0.48442,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9365,ERR3011943,ERX3014403,ERS2994077,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Cyproter1 2,SAMEA5186578,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186578|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Cyproter1 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Cyproter1 2|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:Cyproterone 2 s,Cyproterone 2 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:cyproter1|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_Cyproterone_2_R1.fastq.gz,fastq,1823142918.0,24468337.0,E MTAB 7283:Cyproterone 2,0:74.51 1:0,A:469387174;C:428783310;G:403791044;T:521171021;N:10369,74,0,,,469387174,428783310,403791044,521171021,10369,ERX3014403,ERS2994077,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.9432,,0.11718,,0.67389,,0.4768,,74,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9366,ERR3011942,ERX3014402,ERS2994076,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Cyproter1 1,SAMEA5186577,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186577|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Cyproter1 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Cyproter1 1|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:Cyproterone 1 s,Cyproterone 1 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:cyproter1|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_Cyproterone_1_R1.fastq.gz,fastq,1901027130.0,25512731.0,E MTAB 7283:Cyproterone 1,0:74.51 1:0,A:487302419;C:449208827;G:422183780;T:542321577;N:10527,74,0,,,487302419,449208827,422183780,542321577,10527,ERX3014402,ERS2994076,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94427,,0.11318,,0.67294,,0.47183,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
10161,ERR5385019,ERX5169945,ERS5845164,ERP127328,PRJEB43370,RNA seq of whole zebrafish embryos at 6 and 10hpf,E-MTAB-10167,Other,RNA seq was performed to reveal the RNA expression profile at two different stages shield and tail bud stage in the embryogenesis of zebrafish wild type strain AB. Zebrafish embryos were collected at the shield stage and tail bud stage  which correspond to 6 hpf and 10 hpf  respectively. Total RNA was extracted with miRNeasy Mini Kit  libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina  and paired end sequencing was performed using NovaSeq 6000 Illumina.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Zebrafish embryos obtained from wild type strain AB were collected at the shield stage and tail bud stage  which correspond to 6 hpf and 10 hpf  respectively. Total RNA was extracted with miRNeasy Mini Kit Qiagen  217004 according to the manufacturer's instructions. Quality of extracted RNA was assessed using the NanoDrop ND 1000 Spectrophotometer ThermoFisher Scientific and by agarose gel electrophoresis. Samples were stored at  80 ℃ Libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina according to the manufacturer's instructions.,Danio rerio AB wildtype tail bud stage,SAMEA8158396,"Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University",ENA first public:2021 07 01|ENA last update:2021 07 01|External Id:SAMEA8158396|INSDC center alias:Department of Cellular Regulation  Research Institute for Microbial Diseases  Osaka University|INSDC center name:Department of Cellular Regulation  Research Institute for Microbial Diseases  Osaka University|INSDC first public:2021 07 01T00:11:10Z|INSDC last update:2021 07 01T00:11:10Z|INSDC status:public|Submitter Id:E MTAB 10167:Danio rerio AB wildtype tail bud stage|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 10167:Danio rerio AB wildtype tail bud stage|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of whole zebrafish embryos at 6 and 10hpf,E MTAB 10167:Danio rerio AB wildtype tail bud stage p,Danio rerio AB wildtype tail bud stage p,RNA seq of whole zebrafish embryos at 6 and 10hpf,Zebrafish embryos obtained from wild type strain AB were collected at the shield stage and tail bud stage  which correspond to 6 hpf and 10 hpf  respectively.  Total RNA was extracted with miRNeasy Mini Kit Qiagen  217004 according to the manufacturer's instructions. Quality of extracted RNA was assessed using the NanoDrop ND 1000 Spectrophotometer ThermoFisher Scientific and by agarose gel electrophoresis. Samples were stored at  80 ℃ Libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina according to the manufacturer's instructions.,Experimental Factor: developmental stage:gastrula bud,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP127328,Illumina NovaSeq 6000 paired end sequencing; RNA seq of whole zebrafish embryos at 6 and 10hpf,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,10hpf_Zebrafish_R1.fastq.gz 10hpf_Zebrafish_R2.fastq.gz,fastq fastq,16339887666.0,80890533.0,E MTAB 10167:10hpf Zebrafish R,0:101 1:101,A:4335047391;C:3850067296;G:3827279083;T:4327089161;N:404735,101,101,,,4335047391,3850067296,3827279083,4327089161,404735,ERX5169945,ERS5845164,ERA3502311,"Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University|European Nucleotide Archive","Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University|European Nucleotide Archive",2,0.95781,0.95944,0.09186,0.09149,0.73608,0.73677,0.47851,0.48067,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2021-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
10162,ERR5385018,ERX5169944,ERS5845163,ERP127328,PRJEB43370,RNA seq of whole zebrafish embryos at 6 and 10hpf,E-MTAB-10167,Other,RNA seq was performed to reveal the RNA expression profile at two different stages shield and tail bud stage in the embryogenesis of zebrafish wild type strain AB. Zebrafish embryos were collected at the shield stage and tail bud stage  which correspond to 6 hpf and 10 hpf  respectively. Total RNA was extracted with miRNeasy Mini Kit  libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina  and paired end sequencing was performed using NovaSeq 6000 Illumina.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Zebrafish embryos obtained from wild type strain AB were collected at the shield stage and tail bud stage  which correspond to 6 hpf and 10 hpf  respectively. Total RNA was extracted with miRNeasy Mini Kit Qiagen  217004 according to the manufacturer's instructions. Quality of extracted RNA was assessed using the NanoDrop ND 1000 Spectrophotometer ThermoFisher Scientific and by agarose gel electrophoresis. Samples were stored at  80 ℃ Libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina according to the manufacturer's instructions.,Danio rerio AB wildtype shield stage,SAMEA8158395,"Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University",ENA first public:2021 07 01|ENA last update:2021 07 01|External Id:SAMEA8158395|INSDC center alias:Department of Cellular Regulation  Research Institute for Microbial Diseases  Osaka University|INSDC center name:Department of Cellular Regulation  Research Institute for Microbial Diseases  Osaka University|INSDC first public:2021 07 01T00:11:10Z|INSDC last update:2021 07 01T00:11:10Z|INSDC status:public|Submitter Id:E MTAB 10167:Danio rerio AB wildtype shield stage|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula shield|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 10167:Danio rerio AB wildtype shield stage|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of whole zebrafish embryos at 6 and 10hpf,E MTAB 10167:Danio rerio AB wildtype shield stage p,Danio rerio AB wildtype shield stage p,RNA seq of whole zebrafish embryos at 6 and 10hpf,Zebrafish embryos obtained from wild type strain AB were collected at the shield stage and tail bud stage  which correspond to 6 hpf and 10 hpf  respectively.  Total RNA was extracted with miRNeasy Mini Kit Qiagen  217004 according to the manufacturer's instructions. Quality of extracted RNA was assessed using the NanoDrop ND 1000 Spectrophotometer ThermoFisher Scientific and by agarose gel electrophoresis. Samples were stored at  80 ℃ Libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina according to the manufacturer's instructions.,Experimental Factor: developmental stage:gastrula shield,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP127328,Illumina NovaSeq 6000 paired end sequencing; RNA seq of whole zebrafish embryos at 6 and 10hpf,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,6hpf_Zebrafish_R1.fastq.gz 6hpf_Zebrafish_R2.fastq.gz,fastq fastq,13564619564.0,67151582.0,E MTAB 10167:6hpf Zebrafish R,0:101 1:101,A:3600635755;C:3192954183;G:3191087455;T:3579609049;N:333122,101,101,,,3600635755,3192954183,3191087455,3579609049,333122,ERX5169944,ERS5845163,ERA3502311,"Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University|European Nucleotide Archive","Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University|European Nucleotide Archive",2,0.95783,0.95972,0.08032,0.07998,0.75619,0.75694,0.468,0.48015,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2021-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
11041,ERR9995536,ERX9536682,ERS12521224,ERP138294,PRJEB53494,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing,94bf5509-4622-4d5f-b7c5-6a14bdfac340,Other,RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10,,dRNA seq of 4hpf Zebrafish embryos,Zebrafish dRNA 4hpf,SAMEA110422854,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110422854|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:21:01Z|INSDC last update:2022 10 10T00:21:01Z|INSDC status:public|Submitter Id:Zebrafish dRNA 4hpf|common name:zebrafish|sample name:Zebrafish dRNA 4hpf,,,,,,,,,MinION sequencing,ena EXPERIMENT TAB 27 07 2022 11:41:43:673 3,Zebrafish dRNA 4hpf,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,MinION,,ERP138294,MinION sequencing,ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|instrument model:PromethION,PDBN042841_dRNA_4hpf.tar.gz,nanopore,772304625.0,897768.0,ena RUN TAB 27 07 2022 11:41:43:690 4,0:860.25,A:224977035;C:165273397;G:156659356;T:225394837;N:0,860,,,,224977035,165273397,156659356,225394837,0,ERX9536682,ERS12521224,ERA16500713,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,3prime,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-10-10,Blastula,Embryo,Embryo Imprecise,All anatomical structures
25316,SRR25786849,SRX21509238,SRS18740266,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144 mutant Danio rerio 3 dpf,CD KD 144,,strain:mir 144 mutant|age:3 days|collection date:not provided|geo loc name:not provided|sex:mixed|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq Erythrocytes miR 144 mutant Danio rerio 3 dpf replicate 2,CD KD 1442,CD KD 1442,Libraries were made using Illumina mRNA seq library prep kit,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_KD_1442-R_S4_L001_R2_001.fastq.gz CD_KD_1442-R_S4_L001_R1_001.fastq.gz,fastq fastq,15176751228.0,77119924.0,CD KD 1442 R S4 L001 R1 001.fastq.gz,0:98.43 1:98.37,A:3779746373;C:3784109407;G:3856858311;T:3696705097;N:59332040,98,98,,,3779746373,3784109407,3856858311,3696705097,59332040,SRX21509238,SRS18740266,SRA1701488,University of East Anglia|Biological Sciences,University of East Anglia,2,0.97046,0.97577,0.04054,0.04056,0.84404,0.84368,0.44473,0.44497,99,100,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2023-08-30,Larval,Larval,Whole Organism,All anatomical structures
25317,SRR25786850,SRX21509237,SRS18740266,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144 mutant Danio rerio 3 dpf,CD KD 144,,strain:mir 144 mutant|age:3 days|collection date:not provided|geo loc name:not provided|sex:mixed|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq Erythrocytes miR 144 mutant Danio rerio 3 dpf replicate 1,CD KD 1441,CD KD 1441,Libraries were made using Illumina mRNA seq library prep kit,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_KD_1441-R_S3_L001_R2_001.fastq.gz CD_KD_1441-R_S3_L001_R1_001.fastq.gz,fastq fastq,12981589931.0,66199400.0,CD KD 1441 R S3 L001 R1 001.fastq.gz,0:98.08 1:98.02,A:3222063377;C:3237477192;G:3298955148;T:3151608365;N:71485849,98,98,,,3222063377,3237477192,3298955148,3151608365,71485849,SRX21509237,SRS18740266,SRA1701488,University of East Anglia|Biological Sciences,University of East Anglia,2,0.97163,0.97711,0.03644,0.03649,0.8188,0.81889,0.44686,0.44149,100,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2023-08-30,Larval,Larval,Whole Organism,All anatomical structures
25318,SRR25786851,SRX21509236,SRS18740265,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type Danio rerio 3 dpf,CD KD WT,,strain:Wildtype|age:3 days|collection date:not provided|geo loc name:not provided|sex:mixed|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq Erythrocytes Wild type Danio rerio 3 dpf replicate 2,CD KD WT2,CD KD WT2,Libraries were made using Illumina mRNA seq library prep kit,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_KD_WT2-R_S2_L001_R1_001.fastq.gz CD_KD_WT2-R_S2_L001_R2_001.fastq.gz,fastq fastq,13841850598.0,71086657.0,CD KD WT2 R S2 L001 R1 001.fastq.gz,0:97.39 1:97.33,A:3429992533;C:3433873133;G:3489428993;T:3365505686;N:123050253,97,97,,,3429992533,3433873133,3489428993,3365505686,123050253,SRX21509236,SRS18740265,SRA1701488,University of East Anglia|Biological Sciences,University of East Anglia,2,0.97088,0.97596,0.03787,0.0381,0.84896,0.8496,0.45727,0.45346,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2023-08-30,Larval,Larval,Whole Organism,All anatomical structures
25319,SRR25786852,SRX21509235,SRS18740265,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type Danio rerio 3 dpf,CD KD WT,,strain:Wildtype|age:3 days|collection date:not provided|geo loc name:not provided|sex:mixed|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq Erythrocytes Wild type Danio rerio 3 dpf replicate 1,CD KD WT1,CD KD WT1,Libraries were made using Illumina mRNA seq library prep kit,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_KD_WT1-R_S1_L001_R1_001.fastq.gz CD_KD_WT1-R_S1_L001_R2_001.fastq.gz,fastq fastq,13279321095.0,67105432.0,CD KD WT1 R S1 L001 R1 001.fastq.gz,0:98.98 1:98.91,A:3310018513;C:3313506420;G:3374819099;T:3243710775;N:37266288,98,98,,,3310018513,3313506420,3374819099,3243710775,37266288,SRX21509235,SRS18740265,SRA1701488,University of East Anglia|Biological Sciences,University of East Anglia,2,0.97038,0.97604,0.04235,0.04238,0.83676,0.8367,0.45607,0.45443,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2023-08-30,Larval,Larval,Whole Organism,All anatomical structures
26499,SRR26031755,SRX21749012,SRS18856550,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS rtf1MO 3,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 07 14|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,M3,MO3,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_rtf1MO_3.fastq,fastq,793876754.0,15197870.0,RNAseq hand2FACS rtf1MO 3.fastq,0:52.24,A:208793415;C:174763420;G:174630814;T:235479388;N:209717,52,,,,208793415,174763420,174630814,235479388,209717,SRX21749012,SRS18856550,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.88868,,0.1097,,0.77644,,0.51136,,53,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26500,SRR26031756,SRX21749011,SRS18856545,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS rtf1MO 2,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 07 07|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,M2,MO2,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_rtf1MO_2.fastq,fastq,864787205.0,16568310.0,RNAseq hand2FACS rtf1MO 2.fastq,0:52.20,A:227648729;C:189720880;G:190025417;T:257026454;N:365725,52,,,,227648729,189720880,190025417,257026454,365725,SRX21749011,SRS18856545,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.87433,,0.10781,,0.77366,,0.50792,,53,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26501,SRR26031757,SRX21749010,SRS18856549,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS rtf1MO 1,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 03 04|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,M1,MO1,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_rtf1MO_1.fastq,fastq,821983134.0,15737564.0,RNAseq hand2FACS rtf1MO 1.fastq,0:52.23,A:216610704;C:179969953;G:180145537;T:245093230;N:163710,52,,,,216610704,179969953,180145537,245093230,163710,SRX21749010,SRS18856549,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.88099,,0.09837,,0.78007,,0.50262,,53,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26502,SRR26031758,SRX21749009,SRS18856546,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS control 3,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2020 02 26|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,C3,CTL3,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_control_3.fastq,fastq,880285441.0,16931477.0,RNAseq hand2FACS control 3.fastq,0:51.99,A:233959122;C:192477087;G:190893530;T:262700285;N:255417,51,,,,233959122,192477087,190893530,262700285,255417,SRX21749009,SRS18856546,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.90285,,0.10232,,0.76982,,0.50837,,53,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26503,SRR26031759,SRX21749008,SRS18856548,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS control 2,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2019 12 19|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,C2,CTL2,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_control_2.fastq,fastq,317458963.0,6417814.0,RNAseq hand2FACS control 2.fastq,0:49.47,A:83925064;C:70621123;G:68872886;T:93923129;N:116761,49,,,,83925064,70621123,68872886,93923129,116761,SRX21749008,SRS18856548,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.85587,,0.08493,,0.75558,,0.51678,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
26504,SRR26031760,SRX21749007,SRS18856543,SRP459729,PRJNA1015262,Rtf1 dependent transcriptional pausing regulates cardiogenesis,PRJNA1015262,Other,During heart development  an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II  as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis  we found that Rtf1 is essential for cardiogenesis and that without xxx activity  cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain  which confers interaction with the pausing/elongation factor Spt5  was required for Rtf1's ability to support cardiac progenitor formation  while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP seq and found that Pol II signals at the TSS of genes was reduced  suggesting a reduction in transcriptional pausing. Intriguingly  pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.,,,,,RNAseq hand2FACS control 1,,strain:TgBAChand2:EGFPpd24|dev stage:10 12 somite stage|collection date:2019 11 29|geo loc name:USA:California Los Angeles|sex:n/a|tissue:hand2:GFP positive cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of hand2:GFP positive cells from 10 12 somite stage zebrafish embryos,C1,CTL1,NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina from 5 10 ng input RNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP459729,,,RNAseq_hand2FACS_control_1.fastq,fastq,448273888.0,9055865.0,RNAseq hand2FACS control 1.fastq,0:49.50,A:119317727;C:99863109;G:96352533;T:132659621;N:80898,49,,,,119317727,99863109,96352533,132659621,80898,SRX21749007,SRS18856543,SRA1709841,"University of California, Los Angeles|Molecular, Cell, and Developmental Biology","University of California, Los Angeles",1,0.88622,,0.09573,,0.76086,,0.42689,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
28538,SRR26395012,SRX22100922,SRS19166048,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,50% epiboly Iso seq,,strain:AB x India|age:5.3 hpf|dev stage:50% epiboly|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 10|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: 50% epiboly,DR 010,DR 010,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,50epiboly.ccs.fq.gz,fastq,6994871304.0,1739615.0,50epiboly.ccs.fq.gz,0:4020.93,A:1886646970;C:1618863911;G:1609321304;T:1880039119;N:0,4020,,,,1886646970,1618863911,1609321304,1880039119,0,SRX22100922,SRS19166048,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.2059,,0.00164,,0.92101,,0.06119,,3367,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28539,SRR26395013,SRX22100921,SRS19166047,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,zfs:0000015 Iso seq,,strain:AB x India|age:4.7 hpf|dev stage:zfs:0000015|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 9|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: zfs:0000015,DR 009,DR 009,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,30epiboly.ccs.fq.gz,fastq,5233736965.0,1358516.0,zfs:0000015.ccs.fq.gz,0:3852.54,A:1425421240;C:1199630062;G:1191034759;T:1417650904;N:0,3852,,,,1425421240,1199630062,1191034759,1417650904,0,SRX22100921,SRS19166047,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.40862,,0.00581,,0.86123,,0.47684,,3440,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28540,SRR26395014,SRX22100920,SRS19166046,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,dome Iso seq,,strain:AB x India|age:4.3 hpf|dev stage:dome|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 8|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: dome,DR 008,DR 008,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,dome.ccs.fq.gz,fastq,6426069602.0,1667809.0,dome.ccs.fq.gz,0:3853.00,A:1735630855;C:1486999783;G:1476424228;T:1727014736;N:0,3853,,,,1735630855,1486999783,1476424228,1727014736,0,SRX22100920,SRS19166046,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.20197,,0.00145,,0.91388,,0.06247,,6938,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28541,SRR26395015,SRX22100919,SRS19166045,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,sphere Iso seq,,strain:AB x India|age:4 hpf|dev stage:sphere|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 7|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: sphere,DR 007,DR 007,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,sphere.ccs.fq.gz,fastq,7456522395.0,2030744.0,sphere.ccs.fq.gz,0:3671.82,A:2009379061;C:1725915606;G:1718055774;T:2003171954;N:0,3671,,,,2009379061,1725915606,1718055774,2003171954,0,SRX22100919,SRS19166045,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.41317,,0.00317,,0.85504,,0.46671,,5517,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28542,SRR26395016,SRX22100917,SRS19166043,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield RNA seq rep8,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR sh 8|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: shield replicate8,DR 051,DR 051,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,Shield-8_1.fq.gz Shield-8_2.fq.gz,fastq fastq,15762545120.0,56294804.0,Shield 8 1.fq.gz,0:140 1:140,A:4228709269;C:3695256879;G:3726067176;T:4112463793;N:48003,140,140,,,4228709269,3695256879,3726067176,4112463793,48003,SRX22100917,SRS19166043,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.94979,0.95185,0.07126,0.07102,0.76755,0.76773,0.50529,0.50592,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28543,SRR26395017,SRX22100916,SRS19166042,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,oblong Iso seq,,strain:AB x India|age:3.7 hpf|dev stage:oblong|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 6|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: oblong,DR 006,DR 006,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,oblong.ccs.fq.gz,fastq,5138806264.0,1450821.0,oblong.ccs.fq.gz,0:3542.00,A:1387179645;C:1186984765;G:1181776562;T:1382865292;N:0,3542,,,,1387179645,1186984765,1181776562,1382865292,0,SRX22100916,SRS19166042,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.41494,,0.0019,,0.85267,,0.45513,,8789,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28544,SRR26395018,SRX22100915,SRS19166041,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield RNA seq rep7,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR sh 7|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: shield replicate7,DR 050,DR 050,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,Shield-7_1.fq.gz Shield-7_2.fq.gz,fastq fastq,15398289480.0,54993891.0,Shield 7 1.fq.gz,0:140 1:140,A:4074722797;C:3649035072;G:3682015786;T:3992469036;N:46789,140,140,,,4074722797,3649035072,3682015786,3992469036,46789,SRX22100915,SRS19166041,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95219,0.95373,0.0715,0.0711,0.76313,0.76292,0.49998,0.49568,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28545,SRR26395019,SRX22100914,SRS19166040,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield RNA seq rep6,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR sh 6|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: shield replicate6,DR 049,DR 049,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,Shield-6_1.fq.gz Shield-6_2.fq.gz,fastq fastq,16327179120.0,58311354.0,Shield 6 1.fq.gz,0:140 1:140,A:4372183418;C:3818375443;G:3853553895;T:4283014987;N:51377,140,140,,,4372183418,3818375443,3853553895,4283014987,51377,SRX22100914,SRS19166040,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95316,0.95424,0.05929,0.05845,0.75745,0.75682,0.48626,0.4848,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28546,SRR26395020,SRX22100913,SRS19166039,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield RNA seq rep5,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR sh 5|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: shield replicate5,DR 048,DR 048,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,Shield-5_1.fq.gz Shield-5_2.fq.gz,fastq fastq,15066432920.0,53808689.0,Shield 5 1.fq.gz,0:140 1:140,A:4038093009;C:3519974340;G:3554554998;T:3953765648;N:44925,140,140,,,4038093009,3519974340,3554554998,3953765648,44925,SRX22100913,SRS19166039,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95404,0.95588,0.05759,0.05623,0.76067,0.76025,0.48812,0.4867,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28547,SRR26395021,SRX22100912,SRS19166038,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield RNA seq rep4,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR sh 4|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: shield replicate4,DR 047,DR 047,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,Shield-4_1.fq.gz Shield-4_2.fq.gz,fastq fastq,16536966880.0,59060596.0,Shield 4 1.fq.gz,0:140 1:140,A:4424555246;C:3870128974;G:3905988590;T:4336243381;N:50689,140,140,,,4424555246,3870128974,3905988590,4336243381,50689,SRX22100912,SRS19166038,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95449,0.95538,0.06048,0.05828,0.75737,0.75613,0.47956,0.4814,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28548,SRR26395022,SRX22100911,SRS19166037,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield RNA seq rep3,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR sh 3|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: shield replicate3,DR 046,DR 046,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,Shield-3_1.fq.gz Shield-3_2.fq.gz,fastq fastq,17019618000.0,60784350.0,Shield 3 1.fq.gz,0:140 1:140,A:4575832980;C:3964601842;G:4000470774;T:4478659727;N:52677,140,140,,,4575832980,3964601842,4000470774,4478659727,52677,SRX22100911,SRS19166037,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95355,0.95446,0.0641,0.06282,0.76122,0.7613,0.47036,0.47493,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28549,SRR26395023,SRX22100910,SRS19166035,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield RNA seq rep2,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR sh 2|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: shield replicate2,DR 045,DR 045,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,Shield-2_1.fq.gz Shield-2_2.fq.gz,fastq fastq,16732360960.0,59758432.0,Shield 2 1.fq.gz,0:140 1:140,A:4501751099;C:3892688345;G:3929794118;T:4408076627;N:50771,140,140,,,4501751099,3892688345,3929794118,4408076627,50771,SRX22100910,SRS19166035,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95234,0.95249,0.06482,0.06341,0.75722,0.75615,0.47904,0.47639,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28550,SRR26395024,SRX22100909,SRS19166034,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield RNA seq rep1,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR sh 1|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: shield replicate1,DR 044,DR 044,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,Shield-1_1.fq.gz Shield-1_2.fq.gz,fastq fastq,17928569400.0,64030605.0,Shield 1 1.fq.gz,0:140 1:140,A:4941499556;C:4080333377;G:4110452158;T:4796233689;N:50620,140,140,,,4941499556,4080333377,4110452158,4796233689,50620,SRX22100909,SRS19166034,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.9473,0.95033,0.0571,0.05495,0.76826,0.76743,0.47692,0.48711,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28551,SRR26395025,SRX22100908,SRS19166036,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep8,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 8|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate8,DR 043,DR 043,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-8_1.fq.gz C1K-8_2.fq.gz,fastq fastq,17897176360.0,63918487.0,C1K 8 1.fq.gz,0:140 1:140,A:4746019128;C:4222117801;G:4262745510;T:4666241121;N:52800,140,140,,,4746019128,4222117801,4262745510,4666241121,52800,SRX22100908,SRS19166036,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95626,0.95754,0.02383,0.02273,0.76155,0.76116,0.47882,0.47576,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28552,SRR26395026,SRX22100907,SRS19166033,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep7,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 7|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate7,DR 042,DR 042,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-7_1.fq.gz C1K-7_2.fq.gz,fastq fastq,18354684880.0,65552446.0,C1K 7 1.fq.gz,0:140 1:140,A:4895158722;C:4306679638;G:4342135666;T:4810655169;N:55685,140,140,,,4895158722,4306679638,4342135666,4810655169,55685,SRX22100907,SRS19166033,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95303,0.95677,0.02498,0.02373,0.75893,0.75866,0.47717,0.47879,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28553,SRR26395027,SRX22100906,SRS19166032,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep6,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 6|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate6,DR 041,DR 041,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-6_1.fq.gz C1K-6_2.fq.gz,fastq fastq,19129533360.0,68319762.0,C1K 6 1.fq.gz,0:140 1:140,A:5092659624;C:4497887725;G:4535246152;T:5003683373;N:56486,140,140,,,5092659624,4497887725,4535246152,5003683373,56486,SRX22100906,SRS19166032,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95423,0.95605,0.02565,0.0242,0.76086,0.76108,0.47814,0.47811,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28554,SRR26395028,SRX22100905,SRS19166031,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,high Iso seq,,strain:AB x India|age:3.3 hpf|dev stage:high|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 5|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: high,DR 005,DR 005,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,high.ccs.fq.gz,fastq,6811221417.0,1785766.0,high.ccs.fq.gz,0:3814.17,A:1820349159;C:1592171013;G:1583702800;T:1814998445;N:0,3814,,,,1820349159,1592171013,1583702800,1814998445,0,SRX22100905,SRS19166031,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.42981,,0.00073,,0.86182,,0.47846,,4404,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28555,SRR26395029,SRX22100904,SRS19166030,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep5,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 5|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate5,DR 040,DR 040,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-5_1.fq.gz C1K-5_2.fq.gz,fastq fastq,15372822080.0,54902936.0,C1K 5 1.fq.gz,0:140 1:140,A:4098626531;C:3607276129;G:3638280102;T:4028593737;N:45581,140,140,,,4098626531,3607276129,3638280102,4028593737,45581,SRX22100904,SRS19166030,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95392,0.95707,0.02512,0.02391,0.75921,0.75935,0.4795,0.47195,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28556,SRR26395030,SRX22100903,SRS19166029,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep4,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 4|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate4,DR 039,DR 039,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-4_1.fq.gz C1K-4_2.fq.gz,fastq fastq,20077595440.0,71705698.0,C1K 4 1.fq.gz,0:140 1:140,A:5379901813;C:4687577466;G:4725766166;T:5284289042;N:60953,140,140,,,5379901813,4687577466,4725766166,5284289042,60953,SRX22100903,SRS19166029,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95148,0.95674,0.02629,0.02499,0.76163,0.76155,0.48018,0.47955,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28557,SRR26395031,SRX22100902,SRS19166028,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep3,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 3|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate3,DR 038,DR 038,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-3_1.fq.gz C1K-3_2.fq.gz,fastq fastq,17934590800.0,64052110.0,C1K 3 1.fq.gz,0:140 1:140,A:4787436112;C:4203684173;G:4237881984;T:4705533453;N:55078,140,140,,,4787436112,4203684173,4237881984,4705533453,55078,SRX22100902,SRS19166028,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95381,0.95598,0.03203,0.03053,0.75586,0.75475,0.48144,0.48324,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28558,SRR26395032,SRX22100901,SRS19166027,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep2,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 2|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate2,DR 037,DR 037,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-2_2.fq.gz C1K-2_1.fq.gz,fastq fastq,19274856720.0,68838774.0,C1K 2 1.fq.gz,0:140 1:140,A:5184052449;C:4482949893;G:4518818272;T:5088977570;N:58536,140,140,,,5184052449,4482949893,4518818272,5088977570,58536,SRX22100901,SRS19166027,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95024,0.95418,0.02706,0.02563,0.76159,0.7615,0.47685,0.47835,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28559,SRR26395033,SRX22100900,SRS19166026,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep1,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 1|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate1,DR 036,DR 036,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-1_1.fq.gz C1K-1_2.fq.gz,fastq fastq,16722160840.0,59722003.0,C1K 1 1.fq.gz,0:140 1:140,A:4499833873;C:3886448032;G:3916224310;T:4419604469;N:50156,140,140,,,4499833873,3886448032,3916224310,4419604469,50156,SRX22100900,SRS19166026,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.94949,0.95361,0.02676,0.0253,0.76343,0.76313,0.48343,0.47901,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28560,SRR26395034,SRX22100899,SRS19166025,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell RNA seq rep8,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 8|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 64 cell replicate8,DR 035,DR 035,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C64-8_1.fq.gz C64-8_2.fq.gz,fastq fastq,13755975120.0,50948056.0,C64 8 1.fq.gz,0:135 1:135,A:3658420874;C:3226727105;G:3239474262;T:3628930832;N:2422047,135,135,,,3658420874,3226727105,3239474262,3628930832,2422047,SRX22100899,SRS19166025,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.92463,0.92386,0.0253,0.02389,0.77441,0.77851,0.48196,0.47927,135,135,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28561,SRR26395035,SRX22100898,SRS19166024,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell RNA seq rep7,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 7|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 64 cell replicate7,DR 034,DR 034,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C64-7_1.fq.gz C64-7_2.fq.gz,fastq fastq,14250954780.0,52781314.0,C64 7 1.fq.gz,0:135 1:135,A:3810945650;C:3320623800;G:3339892194;T:3776960886;N:2532250,135,135,,,3810945650,3320623800,3339892194,3776960886,2532250,SRX22100898,SRS19166024,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.93734,0.93685,0.02705,0.02576,0.77553,0.7791,0.47481,0.47745,135,135,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28562,SRR26395036,SRX22100897,SRS19166023,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell RNA seq rep6,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 6|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 64 cell replicate6,DR 033,DR 033,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C64-6_1.fq.gz C64-6_2.fq.gz,fastq fastq,14251193190.0,52782197.0,C64 6 1.fq.gz,0:135 1:135,A:3801408063;C:3332053069;G:3345233238;T:3769986735;N:2512085,135,135,,,3801408063,3332053069,3345233238,3769986735,2512085,SRX22100897,SRS19166023,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.94348,0.94342,0.02571,0.02414,0.77112,0.77492,0.48218,0.4777,135,135,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28563,SRR26395037,SRX22100896,SRS19166022,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell RNA seq rep5,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 5|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 64 cell replicate5,DR 032,DR 032,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C64-5_1.fq.gz C64-5_2.fq.gz,fastq fastq,15142948650.0,56084995.0,C64 5 1.fq.gz,0:135 1:135,A:4031434744;C:3549307228;G:3562636129;T:3996868396;N:2702153,135,135,,,4031434744,3549307228,3562636129,3996868396,2702153,SRX22100896,SRS19166022,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.93753,0.93663,0.02519,0.024,0.77301,0.77674,0.47421,0.46951,135,135,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28564,SRR26395038,SRX22100895,SRS19166021,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell RNA seq rep4,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 4|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 64 cell replicate4,DR 031,DR 031,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C64-4_1.fq.gz C64-4_2.fq.gz,fastq fastq,14488466220.0,53660986.0,C64 4 1.fq.gz,0:135 1:135,A:3863267905;C:3389148218;G:3402037749;T:3831469669;N:2542679,135,135,,,3863267905,3389148218,3402037749,3831469669,2542679,SRX22100895,SRS19166021,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.93879,0.93825,0.02613,0.02437,0.77212,0.77577,0.47796,0.47196,135,135,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28565,SRR26395039,SRX22100894,SRS19166020,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell Iso seq,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 4|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: 1k cell,DR 004,DR 004,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,1k.ccs.fq.gz,fastq,8036121763.0,2087907.0,1k.ccs.fq.gz,0:3848.89,A:2152838341;C:1873567602;G:1863627936;T:2146087884;N:0,3848,,,,2152838341,1873567602,1863627936,2146087884,0,SRX22100894,SRS19166020,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.43117,,0.00077,,0.86352,,0.48891,,2071,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures
28566,SRR26395040,SRX22100893,SRS19166019,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell RNA seq rep3,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 3|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 64 cell replicate3,DR 030,DR 030,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C64-3_1.fq.gz C64-3_2.fq.gz,fastq fastq,16017940620.0,59325706.0,C64 3 1.fq.gz,0:135 1:135,A:4273558549;C:3744205640;G:3760255830;T:4237074764;N:2845837,135,135,,,4273558549,3744205640,3760255830,4237074764,2845837,SRX22100893,SRS19166019,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.93688,0.9383,0.02702,0.02595,0.77433,0.7767,0.47319,0.47413,135,135,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28567,SRR26395041,SRX22100892,SRS19166018,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell RNA seq rep2,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 2|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 64 cell replicate2,DR 029,DR 029,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C64-2_1.fq.gz C64-2_2.fq.gz,fastq fastq,16732836630.0,61973469.0,C64 2 1.fq.gz,0:135 1:135,A:4451249064;C:3924735460;G:3940154978;T:4413679398;N:3017730,135,135,,,4451249064,3924735460,3940154978,4413679398,3017730,SRX22100892,SRS19166018,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.94302,0.94257,0.02459,0.02333,0.77248,0.77479,0.47902,0.47678,135,135,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28568,SRR26395042,SRX22100891,SRS19166017,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell RNA seq rep1,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 1|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 64 cell replicate1,DR 028,DR 028,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C64-1_1.fq.gz C64-1_2.fq.gz,fastq fastq,16459047450.0,60959435.0,C64 1 1.fq.gz,0:135 1:135,A:4391773658;C:3847087464;G:3866793612;T:4350489494;N:2903222,135,135,,,4391773658,3847087464,3866793612,4350489494,2903222,SRX22100891,SRS19166017,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.94676,0.94707,0.02568,0.0244,0.77236,0.77593,0.48374,0.47691,135,135,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28569,SRR26395043,SRX22100890,SRS19166016,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep8,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 8|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate8,DR 027,DR 027,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-8_1.fq.gz C1-8_2.fq.gz,fastq fastq,14524806800.0,51874310.0,C1 8 1.fq.gz,0:140 1:140,A:3808586515;C:3473203895;G:3505848142;T:3737124558;N:43690,140,140,,,3808586515,3473203895,3505848142,3737124558,43690,SRX22100890,SRS19166016,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95859,0.96129,0.01726,0.01698,0.85405,0.85374,0.47349,0.47931,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28570,SRR26395044,SRX22100889,SRS19166015,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep7,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 7|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate7,DR 026,DR 026,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-7_1.fq.gz C1-7_2.fq.gz,fastq fastq,20478629360.0,73137962.0,C1 7 1.fq.gz,0:140 1:140,A:5376265063;C:4892923429;G:4935127460;T:5274249841;N:63567,140,140,,,5376265063,4892923429,4935127460,5274249841,63567,SRX22100889,SRS19166015,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95971,0.96278,0.01686,0.01629,0.85411,0.85387,0.45729,0.47652,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28571,SRR26395045,SRX22100888,SRS19166014,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep6,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 6|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate6,DR 025,DR 025,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-6_1.fq.gz C1-6_2.fq.gz,fastq fastq,16358886880.0,58424596.0,C1 6 1.fq.gz,0:140 1:140,A:4287038412;C:3917335110;G:3953513580;T:4200950421;N:49357,140,140,,,4287038412,3917335110,3953513580,4200950421,49357,SRX22100888,SRS19166014,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.96027,0.96304,0.01855,0.01825,0.84271,0.84285,0.47803,0.47354,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28572,SRR26395046,SRX22100887,SRS19166013,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep5,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 5|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate5,DR 024,DR 024,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-5_1.fq.gz C1-5_2.fq.gz,fastq fastq,17004986600.0,60732095.0,C1 5 1.fq.gz,0:140 1:140,A:4459128776;C:4070413583;G:4104544139;T:4370848562;N:51540,140,140,,,4459128776,4070413583,4104544139,4370848562,51540,SRX22100887,SRS19166013,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95691,0.95965,0.01876,0.01822,0.84003,0.83934,0.47976,0.47873,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28573,SRR26395047,SRX22100886,SRS19166012,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep4,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 4|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate4,DR 023,DR 023,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-4_1.fq.gz C1-4_2.fq.gz,fastq fastq,17516685480.0,62559591.0,C1 4 1.fq.gz,0:140 1:140,A:4618802699;C:4171295741;G:4210242921;T:4516296296;N:47823,140,140,,,4618802699,4171295741,4210242921,4516296296,47823,SRX22100886,SRS19166012,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95994,0.96214,0.01942,0.01842,0.8421,0.84157,0.47848,0.47528,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28574,SRR26395048,SRX22100885,SRS19166011,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep3,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 3|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate3,DR 022,DR 022,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-3_1.fq.gz C1-3_2.fq.gz,fastq fastq,19515282360.0,69697437.0,C1 3 1.fq.gz,0:140 1:140,A:5115977218;C:4670888345;G:4717977881;T:5010379939;N:58977,140,140,,,5115977218,4670888345,4717977881,5010379939,58977,SRX22100885,SRS19166011,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95708,0.95865,0.02126,0.02102,0.84246,0.84216,0.46934,0.47058,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28575,SRR26395049,SRX22100884,SRS19166010,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep2,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 2|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate2,DR 021,DR 021,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-2_1.fq.gz C1-2_2.fq.gz,fastq fastq,20726034000.0,74021550.0,C1 2 1.fq.gz,0:140 1:140,A:5504115856;C:4899295944;G:4943875721;T:5378685883;N:60596,140,140,,,5504115856,4899295944,4943875721,5378685883,60596,SRX22100884,SRS19166010,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95721,0.95927,0.0207,0.01959,0.83287,0.8326,0.47491,0.47327,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28576,SRR26395050,SRX22100883,SRS19166009,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,64 cell Iso seq,,strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 3|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: 64 cell,DR 003,DR 003,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel,,SRP466518,,,cell64_1.ccs.fq.gz cell64_2.ccs.fq.gz,fastq fastq,2829660788.0,1238867.0,cell64 1.ccs.fq.gz,0:2284.07,A:765802910;C:646754322;G:668768985;T:748334571;N:0,2284,,,,765802910,646754322,668768985,748334571,0,SRX22100883,SRS19166009,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.37504,,0.00108,,0.91149,,0.48939,,1913,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
28577,SRR26395052,SRX22100881,SRS19166007,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep1,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 1|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate1,DR 020,DR 020,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-1_1.fq.gz C1-1_2.fq.gz,fastq fastq,17399401600.0,62140720.0,C1 1 1.fq.gz,0:140 1:140,A:4537529281;C:4191810259;G:4227724301;T:4442283593;N:54166,140,140,,,4537529281,4191810259,4227724301,4442283593,54166,SRX22100881,SRS19166007,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.9597,0.96271,0.01629,0.01558,0.83909,0.83818,0.46855,0.46911,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28578,SRR26395053,SRX22100880,SRS19166006,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep8,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 8|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate8,DR 019,DR 019,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-8_1.fq.gz C0-8_2.fq.gz,fastq fastq,18183625040.0,64941518.0,C0 8 1.fq.gz,0:140 1:140,A:4781555399;C:4337050646;G:4373956478;T:4691007549;N:54968,140,140,,,4781555399,4337050646,4373956478,4691007549,54968,SRX22100880,SRS19166006,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95834,0.96072,0.01841,0.01795,0.84577,0.84524,0.4829,0.48081,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28579,SRR26395054,SRX22100879,SRS19166005,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep7,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 7|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate7,DR 018,DR 018,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-7_1.fq.gz C0-7_2.fq.gz,fastq fastq,15161389040.0,54147818.0,C0 7 1.fq.gz,0:140 1:140,A:3994107417;C:3609023200;G:3642319126;T:3915893474;N:45823,140,140,,,3994107417,3609023200,3642319126,3915893474,45823,SRX22100879,SRS19166005,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95744,0.95996,0.01875,0.01807,0.83725,0.83694,0.47055,0.46748,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28580,SRR26395055,SRX22100878,SRS19166004,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep6,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 6|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate6,DR 017,DR 017,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-6_2.fq.gz C0-6_1.fq.gz,fastq fastq,18372330760.0,65615467.0,C0 6 1.fq.gz,0:140 1:140,A:4848831784;C:4365620714;G:4403697790;T:4754124527;N:55945,140,140,,,4848831784,4365620714,4403697790,4754124527,55945,SRX22100878,SRS19166004,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.96339,0.96549,0.01832,0.01765,0.84719,0.84699,0.47322,0.48081,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28581,SRR26395056,SRX22100877,SRS19166003,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep5,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 5|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate5,DR 016,DR 016,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-5_1.fq.gz C0-5_2.fq.gz,fastq fastq,17733025240.0,63332233.0,C0 5 1.fq.gz,0:140 1:140,A:4656835082;C:4237633580;G:4277583056;T:4560919266;N:54256,140,140,,,4656835082,4237633580,4277583056,4560919266,54256,SRX22100877,SRS19166003,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95837,0.95974,0.01811,0.01704,0.85242,0.85184,0.4749,0.47361,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28582,SRR26395057,SRX22100876,SRS19166002,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep4,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 4|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate4,DR 015,DR 015,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-4_1.fq.gz C0-4_2.fq.gz,fastq fastq,17317453440.0,61848048.0,C0 4 1.fq.gz,0:140 1:140,A:4549082241;C:4110729602;G:4198645748;T:4458943221;N:52628,140,140,,,4549082241,4110729602,4198645748,4458943221,52628,SRX22100876,SRS19166002,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.9524,0.95183,0.0196,0.01909,0.84443,0.84429,0.47269,0.47317,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28583,SRR26395058,SRX22100875,SRS19166001,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep3,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 3|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate3,DR 014,DR 014,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-3_1.fq.gz C0-3_2.fq.gz,fastq fastq,20285193040.0,72447118.0,C0 3 1.fq.gz,0:140 1:140,A:5333425678;C:4804605480;G:4928569454;T:5218530436;N:61992,140,140,,,5333425678,4804605480,4928569454,5218530436,61992,SRX22100875,SRS19166001,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95386,0.95151,0.0188,0.01789,0.84226,0.8424,0.48241,0.47074,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28584,SRR26395059,SRX22100874,SRS19166000,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep2,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 2|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate2,DR 013,DR 013,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-2_1.fq.gz C0-2_2.fq.gz,fastq fastq,18750583600.0,66966370.0,C0 2 1.fq.gz,0:140 1:140,A:4964845916;C:4440076965;G:4485931411;T:4859670521;N:58787,140,140,,,4964845916,4440076965,4485931411,4859670521,58787,SRX22100874,SRS19166000,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95711,0.95855,0.02082,0.01977,0.83733,0.83792,0.4711,0.47348,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28585,SRR26395060,SRX22100873,SRS19165999,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep1,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 1|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate1,DR 012,DR 012,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-1_1.fq.gz C0-1_2.fq.gz,fastq fastq,15875566560.0,56698452.0,C0 1 1.fq.gz,0:140 1:140,A:4193265882;C:3760934849;G:3804966904;T:4116350955;N:47970,140,140,,,4193265882,3760934849,3804966904,4116350955,47970,SRX22100873,SRS19165999,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95661,0.9602,0.02103,0.02033,0.84129,0.84092,0.48083,0.47857,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28586,SRR26395062,SRX22100872,SRS19165998,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,Shield Iso seq,,strain:AB x India|age:6 hpf|dev stage:shield|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 11|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: shield,DR 011,DR 011,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,shield.ccs.fq.gz,fastq,7256029471.0,1854553.0,shield.ccs.fq.gz,0:3912.55,A:1984833012;C:1651523494;G:1642156033;T:1977516932;N:0,3912,,,,1984833012,1651523494,1642156033,1977516932,0,SRX22100872,SRS19165998,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.2041,,0.00298,,0.91837,,0.08263,,2962,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
28587,SRR26395063,SRX22100871,SRS19165997,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell Iso seq,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 2|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: 1 cell,DR 002,DR 002,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel,,SRP466518,,,cell1_1.ccs.fq.gz cell1_2.ccs.fq.gz,fastq fastq,2076576705.0,1053386.0,cell1 1.ccs.fq.gz,0:1971.34,A:560055059;C:479061015;G:485136981;T:552323650;N:0,1971,,,,560055059,479061015,485136981,552323650,0,SRX22100871,SRS19165997,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.44892,,0.00258,,0.90114,,0.50832,,32,,B,,usable mapping rate,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28588,SRR26395064,SRX22100870,SRS19165996,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg Iso seq,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 1|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: fertilized egg,DR 001,DR 001,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel,,SRP466518,,,cell0_1.ccs.fq.gz cell0_2.ccs.fq.gz cell0_3.ccs.fq.gz,fastq fastq fastq,3550605210.0,2083545.0,cell0 1.ccs.fq.gz,0:1704.12,A:990393181;C:795168216;G:861389798;T:903654015;N:0,1704,,,,990393181,795168216,861389798,903654015,0,SRX22100870,SRS19165996,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.33296,,0.00275,,0.95548,,0.552,,1155,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
29718,SRR27485663,SRX23156886,SRS20107307,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 1 hpf  rep4,EV06010,EV06010,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06010.R1.fastq.gz,fastq,620142356.0,8227837.0,EV06010.R1.fastq.gz,0:75.37,A:186029536;C:118842640;G:134072972;T:181171903;N:25305,75,,,,186029536,118842640,134072972,181171903,25305,SRX23156886,SRS20107307,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.90656,,0.06918,,0.80192,,0.72472,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Cleavage,Embryo,Whole Organism,All anatomical structures
29721,SRR27485666,SRX23156883,SRS20107304,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 24 hpf  rep4,EV06007,EV06007,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06007.R1.fastq.gz,fastq,758984715.0,10062029.0,EV06007.R1.fastq.gz,0:75.43,A:221215464;C:148997667;G:167225079;T:221520231;N:26274,75,,,,221215464,148997667,167225079,221520231,26274,SRX23156883,SRS20107304,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.90914,,0.18457,,0.77782,,0.38818,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
29722,SRR27485667,SRX23156882,SRS20107303,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 10 hpf  rep4,EV06006,EV06006,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06006.R1.fastq.gz,fastq,734373761.0,9740919.0,EV06006.R1.fastq.gz,0:75.39,A:217249501;C:141011173;G:161749180;T:214341396;N:22511,75,,,,217249501,141011173,161749180,214341396,22511,SRX23156882,SRS20107303,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.902,,0.14583,,0.80937,,0.67478,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Gastrula,Embryo,Whole Organism,All anatomical structures
29723,SRR27485668,SRX23156881,SRS20107302,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 5 hpf  rep4,EV06005,EV06005,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06005.R1.fastq.gz,fastq,776568876.0,10317721.0,EV06005.R1.fastq.gz,0:75.27,A:238745211;C:151859247;G:171793387;T:214113382;N:57649,75,,,,238745211,151859247,171793387,214113382,57649,SRX23156881,SRS20107302,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.87227,,0.14085,,0.81797,,0.72906,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29724,SRR27485669,SRX23156880,SRS20107301,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 3 hpf  rep4,EV06004,EV06004,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06004.R1.fastq.gz,fastq,682509965.0,9050328.0,EV06004.R1.fastq.gz,0:75.41,A:196111480;C:138950038;G:156032208;T:191368964;N:47275,75,,,,196111480,138950038,156032208,191368964,47275,SRX23156880,SRS20107301,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.91494,,0.12926,,0.80044,,0.71156,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29725,SRR27485670,SRX23156879,SRS20107300,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 1 hpf  rep4,EV06003,EV06003,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06003.R1.fastq.gz,fastq,706095550.0,9366364.0,EV06003.R1.fastq.gz,0:75.39,A:204324355;C:140058731;G:159377323;T:202282197;N:52944,75,,,,204324355,140058731,159377323,202282197,52944,SRX23156879,SRS20107300,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.90788,,0.10297,,0.80168,,0.71073,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Cleavage,Embryo,Whole Organism,All anatomical structures
29726,SRR27485671,SRX23156878,SRS20107299,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 24 hpf  rep4,EV06014,EV06014,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06014.R1.fastq.gz,fastq,708984998.0,9425445.0,EV06014.R1.fastq.gz,0:75.22,A:219626080;C:141270902;G:161722995;T:186246245;N:118776,75,,,,219626080,141270902,161722995,186246245,118776,SRX23156878,SRS20107299,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.84881,,0.17975,,0.79693,,0.44149,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
29727,SRR27485672,SRX23156877,SRS20107298,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 10 hpf  rep4,EV06013,EV06013,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06013.R1.fastq.gz,fastq,569494672.0,7557761.0,EV06013.R1.fastq.gz,0:75.35,A:170266388;C:110739260;G:124536859;T:163915551;N:36614,75,,,,170266388,110739260,124536859,163915551,36614,SRX23156877,SRS20107298,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.90037,,0.16195,,0.81308,,0.71641,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Gastrula,Embryo,Whole Organism,All anatomical structures
29728,SRR27485673,SRX23156876,SRS20107297,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 5 hpf  rep4,EV06012,EV06012,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06012.R1.fastq.gz,fastq,612322255.0,8128508.0,EV06012.R1.fastq.gz,0:75.33,A:190142665;C:119966127;G:131824584;T:170353082;N:35797,75,,,,190142665,119966127,131824584,170353082,35797,SRX23156876,SRS20107297,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.89638,,0.12215,,0.8196,,0.79176,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29729,SRR27485674,SRX23156875,SRS20107296,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 3 hpf  rep4,EV06011,EV06011,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06011.R1.fastq.gz,fastq,516168257.0,6849932.0,EV06011.R1.fastq.gz,0:75.35,A:157131780;C:98595108;G:111327650;T:149089977;N:23742,75,,,,157131780,98595108,111327650,149089977,23742,SRX23156875,SRS20107296,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.89456,,0.0693,,0.80306,,0.73611,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29732,SRR27477292,SRX23148655,SRS20099371,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 24 hpf  rep4,EV09007,EV09007,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09007.R1.fastq.gz,fastq,693872355.0,9217545.0,EV09007.R1.fastq.gz,0:75.28,A:207207066;C:136288214;G:150585299;T:199742228;N:49548,75,,,,207207066,136288214,150585299,199742228,49548,SRX23148655,SRS20099371,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.89376,,0.11471,,0.79192,,0.60125,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
29733,SRR27477293,SRX23148654,SRS20099366,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 10 hpf  rep4,EV09006,EV09006,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09006.R1.fastq.gz,fastq,476216388.0,6331468.0,EV09006.R1.fastq.gz,0:75.21,A:146002765;C:93329508;G:104039751;T:132799091;N:45273,75,,,,146002765,93329508,104039751,132799091,45273,SRX23148654,SRS20099366,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.88768,,0.12305,,0.82696,,0.67338,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Gastrula,Embryo,Whole Organism,All anatomical structures
29734,SRR27477294,SRX23148653,SRS20099369,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 5 hpf  rep4,EV09005,EV09005,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09005.R1.fastq.gz,fastq,1231107704.0,16463264.0,EV09005.R1.fastq.gz,0:74.78,A:408948044;C:228823967;G:256397453;T:336404532;N:533708,74,,,,408948044,228823967,256397453,336404532,533708,SRX23148653,SRS20099369,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.84006,,0.08028,,0.80647,,0.73016,,73,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Blastula,Embryo,Whole Organism,All anatomical structures
29735,SRR27477295,SRX23148652,SRS20099365,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 3 hpf  rep4,EV09004,EV09004,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09004.R1.fastq.gz,fastq,471461315.0,6271281.0,EV09004.R1.fastq.gz,0:75.18,A:148103215;C:93173628;G:103496734;T:126647635;N:40103,75,,,,148103215,93173628,103496734,126647635,40103,SRX23148652,SRS20099365,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.87715,,0.11105,,0.80606,,0.74204,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Blastula,Embryo,Whole Organism,All anatomical structures
29736,SRR27477296,SRX23148651,SRS20099370,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 1 hpf  rep4,EV09003,EV09003,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09003.R1.fastq.gz,fastq,438955973.0,5837128.0,EV09003.R1.fastq.gz,0:75.20,A:134628611;C:87460856;G:98199538;T:118638244;N:28724,75,,,,134628611,87460856,98199538,118638244,28724,SRX23148651,SRS20099370,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.89029,,0.11994,,0.80833,,0.72581,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Cleavage,Embryo,Whole Organism,All anatomical structures
30671,SRR28178116,SRX23808192,SRS20631136,SRP492753,PRJNA1082072,Danio rerio Raw sequence reads,PRJNA1082072,Whole Genome Sequencing,RNA seq data of ace function in development,,,ace knock out,,Ace 5dpf,,strain:AB|breed:Artemia|age:5 dpf|collection date:2023 06 20|geo loc name:China|sex:pooled male and female|tissue:Whole embryo|birth date:2023 06 15|genotype:ace / |BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,Ace5,Ace5,RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP492753,,,ace5dpf_1.fq.gz ace5dpf_2.fq.gz,fastq fastq,6270296100.0,20900987.0,ace5dpf 1.fq.gz,0:150 1:150,A:1724295687;C:1427908889;G:1421635888;T:1696367928;N:87708,150,150,,,1724295687,1427908889,1421635888,1696367928,87708,SRX23808192,SRS20631136,SRA1814700,ocean university of China|college of marine life sciences,ocean university of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-01,Larval,Larval,Whole Organism,All anatomical structures
30672,SRR28178117,SRX23808191,SRS20631133,SRP492753,PRJNA1082072,Danio rerio Raw sequence reads,PRJNA1082072,Whole Genome Sequencing,RNA seq data of ace function in development,,,wild type,,WT 5dpf,,strain:AB|breed:Artemia|age:5 dpf|collection date:2023 06 20|geo loc name:China|sex:pooled male and female|tissue:Whole embryo|birth date:2023 06 15|genotype:ace+/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,WT5,WT5,RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP492753,,,WT5dpf_1.fq.gz WT5dpf_2.fq.gz,fastq fastq,6026322000.0,20087740.0,WT5dpf 1.fq.gz,0:150 1:150,A:1657462482;C:1372200290;G:1363936383;T:1632545363;N:177482,150,150,,,1657462482,1372200290,1363936383,1632545363,177482,SRX23808191,SRS20631133,SRA1814700,ocean university of China|college of marine life sciences,ocean university of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-01,Larval,Larval,Whole Organism,All anatomical structures
31890,SRR28743285,SRX24309170,SRS21071681,SRP502786,PRJNA1102287,Zebrafish inppl1a stl445 mutant RNAseq,PRJNA1102287,Other,These are RNAseq data from pooled wild type and inppl1a stl445 Danio rerio mutant whole embryos at 3 dpf,,,inppl1a stl445 mutant sample C,,inppl1a stl445 mutant sample C,,strain:inppl1a mutant C|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 dpf|dev stage:3 dpf|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:whole embryo C|biomaterial provider:GRAY LAB|genotype:inppl1a mutant C|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of inppl1a mutant C,stl445C,stl445C,Novagene,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP502786,,,stl445C_1.fq.gz stl445C_2.fq.gz,fastq fastq,9297920100.0,30993067.0,stl445C 1.fq.gz,0:150 1:150,A:2480150497;C:2183333189;G:2187548387;T:2446422923;N:465104,150,150,,,2480150497,2183333189,2187548387,2446422923,465104,SRX24309170,SRS21071681,SRA1848931,Univeristy of Texas - Dell Pediatrics Reseach Institute|Nutritional Sciences,Univeristy of Texas - Dell Pediatrics Reseach Institute,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-04-19,Larval,Larval,Whole Organism,All anatomical structures
31891,SRR28743286,SRX24309169,SRS21071679,SRP502786,PRJNA1102287,Zebrafish inppl1a stl445 mutant RNAseq,PRJNA1102287,Other,These are RNAseq data from pooled wild type and inppl1a stl445 Danio rerio mutant whole embryos at 3 dpf,,,inppl1a stl445 mutant sample B,,inppl1a stl445 mutant sample B,,strain:inppl1a mutant B|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 dpf|dev stage:3 dpf|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:whole embryo B|biomaterial provider:GRAY LAB|genotype:inppl1a mutant B|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of inppl1a mutant B,stl445B,stl445B,Novagene,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP502786,,,stl445B_1.fq.gz stl445B_2.fq.gz,fastq fastq,7164288900.0,23880963.0,stl445B 1.fq.gz,0:150 1:150,A:1912903566;C:1681545796;G:1688486097;T:1881122778;N:230663,150,150,,,1912903566,1681545796,1688486097,1881122778,230663,SRX24309169,SRS21071679,SRA1848931,Univeristy of Texas - Dell Pediatrics Reseach Institute|Nutritional Sciences,Univeristy of Texas - Dell Pediatrics Reseach Institute,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-04-19,Larval,Larval,Whole Organism,All anatomical structures
31892,SRR28743287,SRX24309168,SRS21071678,SRP502786,PRJNA1102287,Zebrafish inppl1a stl445 mutant RNAseq,PRJNA1102287,Other,These are RNAseq data from pooled wild type and inppl1a stl445 Danio rerio mutant whole embryos at 3 dpf,,,inppl1a stl445 mutant sample A,,inppl1a stl445 mutant sample A,,strain:inppl1a mutant A|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 dpf|dev stage:3 dpf|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:whole embryo A|biomaterial provider:GRAY LAB|genotype:inppl1a mutant A|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of inppl1a mutant A,stl445A,stl445A,Novagene,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP502786,,,stl445A_1.fq.gz stl445A_2.fq.gz,fastq fastq,6509496900.0,21698323.0,stl445A 1.fq.gz,0:150 1:150,A:1721159659;C:1544597555;G:1553920683;T:1689642737;N:176266,150,150,,,1721159659,1544597555,1553920683,1689642737,176266,SRX24309168,SRS21071678,SRA1848931,Univeristy of Texas - Dell Pediatrics Reseach Institute|Nutritional Sciences,Univeristy of Texas - Dell Pediatrics Reseach Institute,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-04-19,Larval,Larval,Whole Organism,All anatomical structures
31893,SRR28743288,SRX24309167,SRS21071677,SRP502786,PRJNA1102287,Zebrafish inppl1a stl445 mutant RNAseq,PRJNA1102287,Other,These are RNAseq data from pooled wild type and inppl1a stl445 Danio rerio mutant whole embryos at 3 dpf,,,AB d3 sample 3,,AB d3 sample 3,,strain:AB wild type 3|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 dpf|dev stage:3 dpf|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:whole embryo 3|biomaterial provider:GRAY LAB|genotype:AB wild type 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of AB wild type 3,AB3,AB3,Novagene,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP502786,,,AB3_1.fq.gz AB3_2.fq.gz,fastq fastq,6003236700.0,20010789.0,AB3 1.fq.gz,0:150 1:150,A:1587549671;C:1423913333;G:1427635736;T:1563843191;N:294769,150,150,,,1587549671,1423913333,1427635736,1563843191,294769,SRX24309167,SRS21071677,SRA1848931,Univeristy of Texas - Dell Pediatrics Reseach Institute|Nutritional Sciences,Univeristy of Texas - Dell Pediatrics Reseach Institute,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-04-19,Larval,Larval,Whole Organism,All anatomical structures
31894,SRR28743289,SRX24309166,SRS21071675,SRP502786,PRJNA1102287,Zebrafish inppl1a stl445 mutant RNAseq,PRJNA1102287,Other,These are RNAseq data from pooled wild type and inppl1a stl445 Danio rerio mutant whole embryos at 3 dpf,,,AB d3 sample 2,,AB d3 sample 2,,strain:AB wild type 2|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 dpf|dev stage:3 dpf|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:whole embryo 2|biomaterial provider:GRAY LAB|genotype:AB wild type 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of AB wild type 2,AB2,AB2,Novagene,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP502786,,,AB2_1.fq.gz AB2_2.fq.gz,fastq fastq,6725792700.0,22419309.0,AB2 1.fq.gz,0:150 1:150,A:1783642195;C:1591564351;G:1592249093;T:1758002304;N:334757,150,150,,,1783642195,1591564351,1592249093,1758002304,334757,SRX24309166,SRS21071675,SRA1848931,Univeristy of Texas - Dell Pediatrics Reseach Institute|Nutritional Sciences,Univeristy of Texas - Dell Pediatrics Reseach Institute,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-04-19,Larval,Larval,Whole Organism,All anatomical structures
31895,SRR28743290,SRX24309165,SRS21071676,SRP502786,PRJNA1102287,Zebrafish inppl1a stl445 mutant RNAseq,PRJNA1102287,Other,These are RNAseq data from pooled wild type and inppl1a stl445 Danio rerio mutant whole embryos at 3 dpf,,,AB d3 sample 1,,AB d3 sample 1,,strain:AB wild type 1|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 dpf|dev stage:3 dpf|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:whole embryo 1|biomaterial provider:GRAY LAB|genotype:AB wild type 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of AB wild type 1,AB1,AB1,Novagene,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP502786,,,AB1_1.fq.gz AB1_2.fq.gz,fastq fastq,7650139500.0,25500465.0,AB1 1.fq.gz,0:150 1:150,A:2028571272;C:1810040115;G:1813654945;T:1997492787;N:380381,150,150,,,2028571272,1810040115,1813654945,1997492787,380381,SRX24309165,SRS21071676,SRA1848931,Univeristy of Texas - Dell Pediatrics Reseach Institute|Nutritional Sciences,Univeristy of Texas - Dell Pediatrics Reseach Institute,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-04-19,Larval,Larval,Whole Organism,All anatomical structures
32437,SRR29249474,SRX24767688,SRS21486855,SRP511062,PRJNA1118794,ABE Ultramax for high efficiency biallelic adenine base editing,PRJNA1118794,Other,RNA off target evaluation,,,,,ABE Umax project RNA off target NGS data,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:2dpf|collection date:2024 01 13|geo loc name:China|sex:pooled male and female|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of injected ABEUmax ex1 only for fig4 and figsupp10,weiq10,weiq10,adapter,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP511062,,,ABEUmax-ex1-only-rep1_R1.fq.gz ABEUmax-ex1-only-rep1_R2.fq.gz,fastq fastq,6282249300.0,20940831.0,ABEUmax ex1 only rep1 R1.fq.gz,0:150 1:150,A:1756899532;C:1390175279;G:1406729636;T:1728418442;N:26411,150,150,,,1756899532,1390175279,1406729636,1728418442,26411,SRX24767688,SRS21486855,SRA1884869,OMRF|Gene and human disease,OMRF,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-05-31,Hatching,Embryo,Whole Organism,All anatomical structures
32438,SRR29249475,SRX24767687,SRS21486855,SRP511062,PRJNA1118794,ABE Ultramax for high efficiency biallelic adenine base editing,PRJNA1118794,Other,RNA off target evaluation,,,,,ABE Umax project RNA off target NGS data,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:2dpf|collection date:2024 01 13|geo loc name:China|sex:pooled male and female|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of injected ABEUmax only for fig4 and figsupp10,weiq9,weiq9,adapter,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP511062,,,ABEUmax-only-rep3_R1.fq.gz ABEUmax-only-rep3_R2.fq.gz,fastq fastq,6410258400.0,21367528.0,ABEUmax only rep3 R1.fq.gz,0:150 1:150,A:1796941092;C:1415805398;G:1424825270;T:1772660117;N:26523,150,150,,,1796941092,1415805398,1424825270,1772660117,26523,SRX24767687,SRS21486855,SRA1884869,OMRF|Gene and human disease,OMRF,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-05-31,Hatching,Embryo,Whole Organism,All anatomical structures
32439,SRR29249476,SRX24767686,SRS21486855,SRP511062,PRJNA1118794,ABE Ultramax for high efficiency biallelic adenine base editing,PRJNA1118794,Other,RNA off target evaluation,,,,,ABE Umax project RNA off target NGS data,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:2dpf|collection date:2024 01 13|geo loc name:China|sex:pooled male and female|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of injected ABEUmax only for fig4 and figsupp10,weiq8,weiq8,adapter,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP511062,,,ABEUmax-only-rep2_R1.fq.gz ABEUmax-only-rep2_R2.fq.gz,fastq fastq,7389619200.0,24632064.0,ABEUmax only rep2 R1.fq.gz,0:150 1:150,A:2026204447;C:1667867375;G:1691882291;T:2003584205;N:80882,150,150,,,2026204447,1667867375,1691882291,2003584205,80882,SRX24767686,SRS21486855,SRA1884869,OMRF|Gene and human disease,OMRF,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-05-31,Hatching,Embryo,Whole Organism,All anatomical structures
32440,SRR29249477,SRX24767685,SRS21486855,SRP511062,PRJNA1118794,ABE Ultramax for high efficiency biallelic adenine base editing,PRJNA1118794,Other,RNA off target evaluation,,,,,ABE Umax project RNA off target NGS data,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:2dpf|collection date:2024 01 13|geo loc name:China|sex:pooled male and female|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of injected ABEUmax only for fig4 and figsupp10,weiq7,weiq7,adapter,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP511062,,,ABEUmax-only-rep1_R1.fq.gz ABEUmax-only-rep1_R2.fq.gz,fastq fastq,11336033400.0,37786778.0,ABEUmax only rep1 R1.fq.gz,0:150 1:150,A:3135246137;C:2536541212;G:2564827351;T:3099296340;N:122360,150,150,,,3135246137,2536541212,2564827351,3099296340,122360,SRX24767685,SRS21486855,SRA1884869,OMRF|Gene and human disease,OMRF,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-05-31,Hatching,Embryo,Whole Organism,All anatomical structures
32441,SRR29249478,SRX24767684,SRS21486855,SRP511062,PRJNA1118794,ABE Ultramax for high efficiency biallelic adenine base editing,PRJNA1118794,Other,RNA off target evaluation,,,,,ABE Umax project RNA off target NGS data,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:2dpf|collection date:2024 01 13|geo loc name:China|sex:pooled male and female|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of injected ABE8e only for fig4 and figsupp10,weiq6,weiq6,adapter,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP511062,,,ABE8e-only-rep3_R1.fq.gz ABE8e-only-rep3_R2.fq.gz,fastq fastq,5719869600.0,19066232.0,ABE8e only rep3 R1.fq.gz,0:150 1:150,A:1608480551;C:1257475652;G:1266100141;T:1587789911;N:23345,150,150,,,1608480551,1257475652,1266100141,1587789911,23345,SRX24767684,SRS21486855,SRA1884869,OMRF|Gene and human disease,OMRF,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-05-31,Hatching,Embryo,Whole Organism,All anatomical structures
32442,SRR29249479,SRX24767683,SRS21486855,SRP511062,PRJNA1118794,ABE Ultramax for high efficiency biallelic adenine base editing,PRJNA1118794,Other,RNA off target evaluation,,,,,ABE Umax project RNA off target NGS data,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:2dpf|collection date:2024 01 13|geo loc name:China|sex:pooled male and female|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of injected ABE8e only for fig4 and figsupp10,weiq5,weiq5,adapter,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP511062,,,ABE8e-only-rep2_R1.fq.gz ABE8e-only-rep2_R2.fq.gz,fastq fastq,7391481300.0,24638271.0,ABE8e only rep2 R1.fq.gz,0:150 1:150,A:2037764745;C:1665759801;G:1685514060;T:2002411849;N:30845,150,150,,,2037764745,1665759801,1685514060,2002411849,30845,SRX24767683,SRS21486855,SRA1884869,OMRF|Gene and human disease,OMRF,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-05-31,Hatching,Embryo,Whole Organism,All anatomical structures
32443,SRR29249480,SRX24767682,SRS21486855,SRP511062,PRJNA1118794,ABE Ultramax for high efficiency biallelic adenine base editing,PRJNA1118794,Other,RNA off target evaluation,,,,,ABE Umax project RNA off target NGS data,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:2dpf|collection date:2024 01 13|geo loc name:China|sex:pooled male and female|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of injected ABEUmax ex2+tp53 gRNA for figsupp10,weiq39,weiq39,adapter,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP511062,,,ABEUmax-ex2-tp53-rep3_R1.fq.gz ABEUmax-ex2-tp53-rep3_R2.fq.gz,fastq fastq,5803077300.0,19343591.0,ABEUmax ex2 tp53 rep3 R1.fq.gz,0:150 1:150,A:1617761226;C:1287691319;G:1296461744;T:1601139422;N:23589,150,150,,,1617761226,1287691319,1296461744,1601139422,23589,SRX24767682,SRS21486855,SRA1884869,OMRF|Gene and human disease,OMRF,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-05-31,Hatching,Embryo,Whole Organism,All anatomical structures