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 306,DRR224536,DRX214821,DRS236344,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 40hpf C,SAMD00222567,,sample name:40hpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222567,DRX214821,40hpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222567,,,,14926054400.0,74630272.0,DRR224536,0:100 1:100,A:3647365116;C:3826172690;G:3866071867;T:3586333511;N:111216,100,100,,,3647365116,3826172690,3866071867,3586333511,111216,DRX214821,DRS236344,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96395,0.96168,0.05081,0.04957,0.75489,0.75607,0.51046,0.52135,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure 307,DRR224535,DRX214820,DRS236343,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 40hpf B,SAMD00222566,,sample name:40hpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222566,DRX214820,40hpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222566,,,,14413995800.0,72069979.0,DRR224535,0:100 1:100,A:3598207137;C:3642219692;G:3750145663;T:3423315835;N:107473,100,100,,,3598207137,3642219692,3750145663,3423315835,107473,DRX214820,DRS236343,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97396,0.97107,0.04686,0.04549,0.7444,0.74968,0.50051,0.49798,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure 308,DRR224534,DRX214819,DRS236342,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 40hpf A,SAMD00222565,,sample name:40hpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222565,DRX214819,40hpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222565,,,,14351831800.0,71759159.0,DRR224534,0:100 1:100,A:3552114377;C:3639389412;G:3719404253;T:3440817088;N:106670,100,100,,,3552114377,3639389412,3719404253,3440817088,106670,DRX214819,DRS236342,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96606,0.96569,0.04249,0.04107,0.7514,0.75367,0.49762,0.49753,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure 309,DRR224533,DRX214818,DRS236341,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 32hpf C,SAMD00222564,,sample name:32hpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222564,DRX214818,32hpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222564,,,,18499667800.0,92498339.0,DRR224533,0:100 1:100,A:4655671152;C:4605325822;G:4688156846;T:4550378341;N:135639,100,100,,,4655671152,4605325822,4688156846,4550378341,135639,DRX214818,DRS236341,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9673,0.96864,0.04184,0.04008,0.73087,0.73318,0.48331,0.48043,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure 310,DRR224532,DRX214817,DRS236340,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 32hpf B,SAMD00222563,,sample name:32hpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222563,DRX214817,32hpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222563,,,,19952418000.0,99762090.0,DRR224532,0:100 1:100,A:4972665902;C:5012518349;G:5094132814;T:4872951533;N:149402,100,100,,,4972665902,5012518349,5094132814,4872951533,149402,DRX214817,DRS236340,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97325,0.97252,0.03729,0.03575,0.71591,0.7163,0.47191,0.47859,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure 311,DRR224531,DRX214816,DRS236339,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 32hpf A,SAMD00222562,,sample name:32hpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222562,DRX214816,32hpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222562,,,,16357024800.0,81785124.0,DRR224531,0:100 1:100,A:4049805675;C:4130985751;G:4172952730;T:4003159212;N:121432,100,100,,,4049805675,4130985751,4172952730,4003159212,121432,DRX214816,DRS236339,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97046,0.96886,0.03577,0.03489,0.73257,0.73231,0.4825,0.48849,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure 10068,ERR4844843,ERX4714625,ERS5338302,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],wt rep2,SAMEA7579966,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579966|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:wt rep2|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:wt rep2|strain:Ab / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:wt rep2 s,wt rep2 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,wt_rep2.fastq.gz,fastq,3456340392.0,34221192.0,E MTAB 9777:wt rep2,0:101 1:0,A:850781866;C:827613239;G:837337477;T:936245388;N:4362422,101,0,,,850781866,827613239,837337477,936245388,4362422,ERX4714625,ERS5338302,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94198,,0.05681,,0.69613,,0.46685,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 10069,ERR4844842,ERX4714624,ERS5338301,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],wt rep1,SAMEA7579965,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579965|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:wt rep1|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:wt rep1|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:wt rep1 s,wt rep1 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,wt_rep1.fastq.gz,fastq,5640822932.0,55849732.0,E MTAB 9777:wt rep1,0:101 1:0,A:1394470185;C:1346058952;G:1354472388;T:1538701573;N:7119834,101,0,,,1394470185,1346058952,1354472388,1538701573,7119834,ERX4714624,ERS5338301,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94371,,0.05678,,0.69664,,0.47233,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 10070,ERR4844841,ERX4714623,ERS5338300,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],foxk MO rep2,SAMEA7579964,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579964|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:foxk MO rep2|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:foxk MO rep2|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:foxk MO rep2 s,foxk MO rep2 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],Experimental Factor: compound:morpholino against foxk1/foxk2/foxk2 1|Experimental Factor: dose:9,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,foxk1-2_rep2.fastq.gz,fastq,3550070715.0,35149215.0,E MTAB 9777:foxk MO rep2,0:101 1:0,A:901160433;C:835963324;G:840839574;T:967604789;N:4502595,101,0,,,901160433,835963324,840839574,967604789,4502595,ERX4714623,ERS5338300,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94006,,0.07603,,0.69455,,0.46867,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 10071,ERR4844840,ERX4714622,ERS5338299,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],foxk MO rep1,SAMEA7579963,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579963|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:foxk MO rep1|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:foxk MO rep1|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:foxk MO rep1 s,foxk MO rep1 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],Experimental Factor: compound:morpholino against foxk1/foxk2/foxk2 1|Experimental Factor: dose:9,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,foxk1-2_rep1.fastq.gz,fastq,3601987139.0,35663239.0,E MTAB 9777:foxk MO rep1,0:101 1:0,A:910641017;C:846039018;G:853351642;T:987409698;N:4545764,101,0,,,910641017,846039018,853351642,987409698,4545764,ERX4714622,ERS5338299,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.93784,,0.08061,,0.69292,,0.47364,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 29799,SRR27437217,SRX23109548,SRS20064321,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,ZEA2 3,,strain:not applicable|isolate:treatment2 3 treat with 1500 ug L 1 zearalen1|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,zearalen11500 3,Z23,Z23,treatment2 3 treat with 1500 ug L 1 zearalenone,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,ZEA2-3_1.fq.gz ZEA2-3_2.fq.gz,fastq fastq,8921721300.0,29739071.0,ZEA2 3 1.fq.gz,0:150 1:150,A:2396882078;C:2056732692;G:2063840198;T:2404120213;N:146119,150,150,,,2396882078,2056732692,2063840198,2404120213,146119,SRX23109548,SRS20064321,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 29800,SRR27437218,SRX23109547,SRS20064320,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,ZEA2 2,,strain:not applicable|isolate:treatment2 2 treat with 1500 ug L 1 zearalen1|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,zearalen11500 2,Z22,Z22,treatment2 2 treat with 1500 ug L 1 zearalenone,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,ZEA2-2_1.fq.gz ZEA2-2_2.fq.gz,fastq fastq,9727978500.0,32426595.0,ZEA2 2 1.fq.gz,0:150 1:150,A:2608560566;C:2245726833;G:2251798776;T:2621800066;N:92259,150,150,,,2608560566,2245726833,2251798776,2621800066,92259,SRX23109547,SRS20064320,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 29801,SRR27437219,SRX23109546,SRS20064319,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,ZEA2 1,,strain:not applicable|isolate:treatment2 1 treat with 1500 ug L 1 zearalen1|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,zearalen11500 1,Z21,Z21,treatment2 1 treat with 1500 ug L 1 zearalenone,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,ZEA2-1_1.fq.gz ZEA2-1_2.fq.gz,fastq fastq,8431396200.0,28104654.0,ZEA2 1 1.fq.gz,0:150 1:150,A:2267734322;C:1940186692;G:1951582614;T:2271799255;N:93317,150,150,,,2267734322,1940186692,1951582614,2271799255,93317,SRX23109546,SRS20064319,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 29802,SRR27437220,SRX23109545,SRS20064318,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,ZEA1 3,,strain:not applicable|isolate:treatment1 3 treat with 1000 ug L 1 zearalen1|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,zearalen11000 3,Z13,Z13,treatment1 3 treat with 1000 ug L 1 zearalenone,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,ZEA1-3_1.fq.gz ZEA1-3_2.fq.gz,fastq fastq,5874342600.0,19581142.0,ZEA1 3 1.fq.gz,0:150 1:150,A:1573493882;C:1359292789;G:1363396567;T:1578061905;N:97457,150,150,,,1573493882,1359292789,1363396567,1578061905,97457,SRX23109545,SRS20064318,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 29803,SRR27437221,SRX23109544,SRS20064317,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,ZEA1 2,,strain:not applicable|isolate:treatment1 2 treat with 1000 ug L 1 zearalen1|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,zearalen11000 2,Z12,Z12,treatment1 2 treat with 1000 ug L 1 zearalenone,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,ZEA1-2_1.fq.gz ZEA1-2_2.fq.gz,fastq fastq,9491685300.0,31638951.0,ZEA1 2 1.fq.gz,0:150 1:150,A:2540695155;C:2193943225;G:2202881363;T:2554070204;N:95353,150,150,,,2540695155,2193943225,2202881363,2554070204,95353,SRX23109544,SRS20064317,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 29804,SRR27437222,SRX23109543,SRS20064316,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,ZEA1 1,,strain:not applicable|isolate:treatment1 1 treat with 1000 ug L 1 zearalen1|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,zearalen11000 1,Z11,Z11,treatment1 1 treat with 1000 ug L 1 zearalenone,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,ZEA1-1_1.fq.gz ZEA1-1_2.fq.gz,fastq fastq,5776274400.0,19254248.0,ZEA1 1 1.fq.gz,0:150 1:150,A:1548868249;C:1335432962;G:1337666172;T:1554211084;N:95933,150,150,,,1548868249,1335432962,1337666172,1554211084,95933,SRX23109543,SRS20064316,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 29805,SRR27437223,SRX23109542,SRS20064315,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,CON0 3,,strain:not applicable|isolate:control3 treat with 0.025% DMSO|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control3,C03,C03,control3 treat with 0.025% DMSO,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,CON0-3_1.fq.gz CON0-3_2.fq.gz,fastq fastq,6281543100.0,20938477.0,CON0 3 1.fq.gz,0:150 1:150,A:1683916255;C:1451185015;G:1455183365;T:1691154944;N:103521,150,150,,,1683916255,1451185015,1455183365,1691154944,103521,SRX23109542,SRS20064315,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 29806,SRR27437224,SRX23109541,SRS20064314,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,CON0 2,,strain:not applicable|isolate:control2 treat with 0.025% DMSO|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control2,C02,C02,control2 treat with 0.025% DMSO,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,CON0-2_1.fq.gz CON0-2_2.fq.gz,fastq fastq,6090834300.0,20302781.0,CON0 2 1.fq.gz,0:150 1:150,A:1629296363;C:1409553283;G:1414998909;T:1636884148;N:101597,150,150,,,1629296363,1409553283,1414998909,1636884148,101597,SRX23109541,SRS20064314,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 29807,SRR27437225,SRX23109540,SRS20064313,SRP482087,PRJNA1061474,Transcriptional sequencing of zearalenone treated zebrafish embryos,PRJNA1061474,Other,To identify the key genes involved in zearalenone toxicity. Transcriptomics analysis was performed.,,,,,CON0 1,,strain:not applicable|isolate:control1 treat with 0.025% DMSO|breed:not collected|cultivar:not applicable|ecotype:not collected|age:24 hpf|dev stage:24 hpf|collection date:not collected|geo loc name:not collected|sex:not collected|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control1,C01,C01,control1 treat with 0.025% DMSO,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482087,,,CON0-1_1.fq.gz CON0-1_2.fq.gz,fastq fastq,6136698900.0,20455663.0,CON0 1 1.fq.gz,0:150 1:150,A:1647513440;C:1414272227;G:1415793921;T:1659016996;N:102316,150,150,,,1647513440,1414272227,1415793921,1659016996,102316,SRX23109540,SRS20064313,SRA1780284,Sichuan Agricultural University|Animal Nutrition Institute,Sichuan Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures 38358,SRR1790101,SRX866154,SRS837238,SRP053202,PRJNA274440,Danio rerio strain:ZF4 cell Transcriptome or Gene expression,PRJNA274440,Other,Zebrafish ZF4 cell exposed to MMS.,,,zebrafish ZF4 cell exposed to PBS at xxxh control group,PBS,PBS,,strain:ZF4|age:24h|sex:not applicable|tissue:1 dpf zebrafish embryos|treatment:PBS control|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish ZF4 cell post PBS treatment at 24h,PBS,PBS,Library construction: Illumina HiSeq 2000 protocol. Experimental design: MMS Sigma USA was dissolved in phosphate buffered saline PBS just before use. Zebrafish ZF4 cells ATCC CRL 2050 derived from 1 dpf zebrafish embryos were routinely maintained in a humidified chamber 28C 5% CO2 in DMEM/F 12 medium GIBICO USA with 10% v/v fetal bovine serum GIBICO USA 100 U/ml penicillin and 100 mg/ml streptomycin GIBICO USA. When confluence reached 70–80 % cells were treated with 639.16μM MMS or an equal volume of PBS control group and incubated for 24 h. Cells were washed 3 times with cold PBS and detached from the culture plate using trypsin GIBICO USA for further experiments.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2000,1800Application ReadForward11Application ReadReverse91,SRP053202,,,PBS_L1_2.fq.gz PBS_L1_1.fq.gz,fastq fastq,4633368120.0,25740934.0,PBS,,,,,,,,,,,,SRX866154,SRS837238,SRA236279,Institute of hydrobiology Chinese academy of scie|Protein Engineering,Institute of hydrobiology Chinese academy of sciences,2,0.9231,0.91127,0.12733,0.12547,0.73547,0.7371,0.54875,0.54758,90,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2016-02-04,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 38359,SRR1789379,SRX865976,SRS837148,SRP053202,PRJNA274440,Danio rerio strain:ZF4 cell Transcriptome or Gene expression,PRJNA274440,Other,Zebrafish ZF4 cell exposed to MMS.,,,zebrafish ZF4 cell post MMS treatment at 24h,MMS,MMS,,strain:ZF4|age:24h|sex:missing|tissue:1 dpf zebrafish embryos|cell line:ZF4|BioSampleModel:Model organism or animal,,,,,,,,,The toxicogenomic response of ZF4 cells to methyl methanesulfonate,zebrafish ZF4 cell exposed to MMS,MMS,Library construction: Illumina HiSeq 2000 protocol. Experimental design: MMS Sigma USA was dissolved in phosphate buffered saline PBS just before use. Zebrafish ZF4 cells ATCC CRL 2050 derived from 1 dpf zebrafish embryos were routinely maintained in a humidified chamber 28C 5% CO2 in DMEM/F 12 medium GIBICO USA with 10% v/v fetal bovine serum GIBICO USA 100 U/ml penicillin and 100 mg/ml streptomycin GIBICO USA. When confluence reached 70–80 % cells were treated with 639.16μM MMS or an equal volume of PBS control group and incubated for 24 h. Cells were washed 3 times with cold PBS and detached from the culture plate using trypsin GIBICO USA for further experiments.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2000,1800Application ReadForward11Application ReadReverse91,SRP053202,,,MMS_L1_1.fq.gz MMS_L1_2.fq.gz,fastq fastq,4836388500.0,26868825.0,Zebrafish ZF4 cell expoused to MMS,0:90 1:90,A:1311355914;C:1078740323;G:1136692368;T:1309518802;N:81093,90,90,,,1311355914,1078740323,1136692368,1309518802,81093,SRX865976,SRS837148,SRA236279,Institute of hydrobiology Chinese academy of scie|Protein Engineering,Institute of hydrobiology Chinese academy of sciences,2,0.93126,0.9293,0.13504,0.13462,0.74008,0.74253,0.55923,0.53956,90,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2016-02-04,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 40984,SRR3521412,SRX1763130,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio: S1 data,S1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,S1_replicate1.fq.gz,fastq,3198275111.0,46580204.0,S1 replicate 1,0:4 1:64.66,A:903404566;C:767156853;G:800702475;T:727011217;N:0,4,64,,,903404566,767156853,800702475,727011217,0,SRX1763130,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.72262,,0.05785,,0.76552,,0.50263,,61,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2016-05-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 40985,SRR3521413,SRX1763130,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio: S1 data,S1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,S1_replicate2.fq.gz,fastq,3458893385.0,48723018.0,S1 replicate 2,0:4 1:66.99,A:1012209805;C:783264940;G:815198929;T:848219711;N:0,4,66,,,1012209805,783264940,815198929,848219711,0,SRX1763130,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.80213,,0.06798,,0.76836,,0.50977,,64,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2017-05-16,Pharyngula,Embryo,Whole Organism,All anatomical structures 40986,SRR3521414,SRX1763130,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio: S1 data,S1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,S1_replicate3.fq.gz,fastq,2246373759.0,27629374.0,S1 replicate 3,0:4 1:77.30,A:680882972;C:506454752;G:543187806;T:515848229;N:0,4,77,,,680882972,506454752,543187806,515848229,0,SRX1763130,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.75362,,0.08102,,0.80874,,0.50576,,43,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2016-05-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 40987,SRR3521415,SRX1763130,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio: S1 data,S1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,,,3113059012.0,39573890.0,S1 replicate 4,0:4 1:74.66,A:917116196;C:724979517;G:776099987;T:694863312;N:0,4,74,,,917116196,724979517,776099987,694863312,0,SRX1763130,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.75652,,0.07876,,0.81385,,0.50701,,69,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2016-05-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 40988,SRR3521416,SRX1763130,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio: S1 data,S1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,S1_replicate5.fq.gz,fastq,3997589784.0,50540637.0,S1 replicate 5,0:4 1:75.10,A:1185172057;C:921610580;G:981479162;T:909327985;N:0,4,75,,,1185172057,921610580,981479162,909327985,0,SRX1763130,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.77298,,0.08278,,0.80196,,0.50419,,122,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2016-05-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 40989,SRR3521417,SRX1763130,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio: S1 data,S1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,loader:fastq load.py,S1_nonCodingRNA1.fq.gz,fastq,2515453735.0,26514293.0,S1 non coding RNA 1,0:94.87,A:545495988;C:609885515;G:774432484;T:585639748;N:0,94,,,,545495988,609885515,774432484,585639748,0,SRX1763130,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.00845,,0.0053,,0.9976,,0.34551,,112,,T,,under 1.2% mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2017-10-02,Pharyngula,Embryo,Whole Organism,All anatomical structures 40990,SRR3521418,SRX1763130,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio: S1 data,S1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,loader:fastq load.py,,,923856697.0,17302758.0,S1 non coding RNA 2,0:53.39,A:249661089;C:215235054;G:243253253;T:215639847;N:67454,53,,,,249661089,215235054,243253253,215639847,67454,SRX1763130,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.10161,,0.02132,,0.98435,,0.29096,,51,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2017-10-02,Pharyngula,Embryo,Whole Organism,All anatomical structures 40991,SRR3521419,SRX1763130,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio: S1 data,S1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,,,797557294.0,14312934.0,S1 non coding RNA 3,0:4 1:51.72,A:215288442;C:189620793;G:209773713;T:182874346;N:0,4,51,,,215288442,189620793,209773713,182874346,0,SRX1763130,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.09688,,0.01835,,0.98027,,0.29048,,75,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2016-05-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 40992,SRR3521405,SRX1763129,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio,V1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,V1_replicate1.fq.gz,fastq,4530127185.0,55155258.0,V1 replicate 1,0:4 1:78.13,A:1262427584;C:1070775955;G:1144547430;T:1052376216;N:0,4,78,,,1262427584,1070775955,1144547430,1052376216,0,SRX1763129,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.74907,,0.09071,,0.7876,,0.57031,,5,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2016-05-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 40993,SRR3521406,SRX1763129,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio,V1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,V1_replicate2.fq.gz,fastq,1189043570.0,25178053.0,V1 replicate 2,0:4 1:43.23,A:319718349;C:286808587;G:313734800;T:268781834;N:0,4,43,,,319718349,286808587,313734800,268781834,0,SRX1763129,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.45251,,0.06891,,0.80385,,0.50742,,143,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2016-05-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 40994,SRR3521407,SRX1763129,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio,V1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,V1_replicate3.fq.gz,fastq,3554365020.0,38155820.0,V1 replicate 3,0:4 1:89.15,A:1029602890;C:801334700;G:876594681;T:846832749;N:0,4,89,,,1029602890,801334700,876594681,846832749,0,SRX1763129,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.68437,,0.09576,,0.81688,,0.53109,,94,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2017-05-16,Pharyngula,Embryo,Whole Organism,All anatomical structures 40995,SRR3521408,SRX1763129,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio,V1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,,,4005348870.0,44573054.0,V1 replicate 4,0:4 1:85.86,A:1152986833;C:913529601;G:1003588263;T:935244173;N:0,4,85,,,1152986833,913529601,1003588263,935244173,0,SRX1763129,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.65253,,0.09144,,0.82726,,0.52272,,87,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2016-05-17,Pharyngula,Embryo,Whole Organism,All anatomical structures 40996,SRR3521409,SRX1763129,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio,V1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,,V1_replicate5.fq.gz,fastq,3724196991.0,41897201.0,V1 replicate 5,0:4 1:84.89,A:1058600798;C:857924228;G:938831956;T:868840009;N:0,4,84,,,1058600798,857924228,938831956,868840009,0,SRX1763129,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.6539,,0.08809,,0.82264,,0.525,,60,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2017-05-16,Pharyngula,Embryo,Whole Organism,All anatomical structures 40997,SRR3521410,SRX1763129,SRS1437887,SRP075186,PRJNA321644,Danio rerio RNA structure,PRJNA321644,Whole Genome Sequencing,RNA structure of Danio rerio to understand role of secondary structure dynamics,,,,Danio rerio transcriptome secondary structure,ASWT RNA structure,,strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal,,,,,,,,,Structure dynamics of zebrafish transcriptome using PAR CLIP,RNA structure of Danio rerio,V1,1,,,OTHER,TRANSCRIPTOMIC,PolyA,SINGLE,ION_TORRENT,Ion Torrent Proton,00Technical ReadAdapter11Application ReadForward5,SRP075186,,loader:fastq load.py,V1_nonCodingRNA.fq.gz,fastq,1824118507.0,29210555.0,V1 non coding RNA,0:62.45,A:473289902;C:444879325;G:490109158;T:415840122;N:0,62,,,,473289902,444879325,490109158,415840122,0,SRX1763129,SRS1437887,SRA425688,CSIR-IGIB,CSIR- Institute of Genomics and Integrative Biology,1,0.08263,,0.01578,,0.98021,,0.34484,,62,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2017-10-02,Pharyngula,Embryo,Whole Organism,All anatomical structures 49338,SRR7891984,SRX4729614,SRS3812052,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP Negative sample2 Lane4,15.I2 24 gfpNeg 2 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP Negative sample2 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP Negative sample2 Lane4,15.I2 24 gfpNeg 2 Lane4,15.I2 24 gfpNeg 2 Lane4,mH2A2 24hpf GFP Negative sample2 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,15.I2-24-gfpNeg-2-Lane4-R1.fastq 15.I2-24-gfpNeg-2-Lane4-R2.fastq,fastq fastq,447724048.0,2968812.0,15.I2 24 gfpNeg 2 Lane4 R1.fastq,0:75.47 1:75.34,A:114878984;C:107107384;G:110724084;T:114765668;N:247928,75,75,,,114878984,107107384,110724084,114765668,247928,SRX4729614,SRS3812052,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.89226,0.89616,0.04911,0.04748,0.79318,0.79555,0.46204,0.47669,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49339,SRR7891985,SRX4729613,SRS3812051,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 75% epiboly whole embryo sample1 Lane3,1.I1 ep wy 1 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 75% epiboly whole embryo sample1 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 75% epiboly whole embryo sample1 Lane3,1.I1 ep wy 1 Lane3,1.I1 ep wy 1 Lane3,mH2A1 75% epiboly whole embryo sample1 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,1.I1-ep-wy-1-Lane3-R1.fastq 1.I1-ep-wy-1-Lane3-R2.fastq,fastq fastq,459481232.0,3044608.0,1.I1 ep wy 1 Lane3 R1.fastq,0:75.49 1:75.42,A:125724225;C:102247136;G:106552305;T:124676614;N:280952,75,75,,,125724225,102247136,106552305,124676614,280952,SRX4729613,SRS3812051,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.86349,0.86857,0.11814,0.11705,0.78358,0.78455,0.53664,0.54034,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49340,SRR7891986,SRX4729612,SRS3812050,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 75% epiboly whole embryo sample1 Lane4,1.I1 ep wy 1 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 75% epiboly whole embryo sample1 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 75% epiboly whole embryo sample1 Lane4,1.I1 ep wy 1 Lane4,1.I1 ep wy 1 Lane4,mH2A1 75% epiboly whole embryo sample1 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,1.I1-ep-wy-1-Lane4-R1.fastq 1.I1-ep-wy-1-Lane4-R2.fastq,fastq fastq,444907371.0,2948130.0,1.I1 ep wy 1 Lane4 R2.fastq,0:75.49 1:75.42,A:121965487;C:98997739;G:102792773;T:120892482;N:258890,75,75,,,121965487,98997739,102792773,120892482,258890,SRX4729612,SRS3812050,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.86608,0.8716,0.11929,0.11696,0.78354,0.7863,0.54273,0.53562,75,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49344,SRR7891990,SRX4729608,SRS3812046,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 75% epiboly whole embryo without xxx sample1 Lane4,2.I1 ep woy 1 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 75% epiboly whole embryo without xxx sample1 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 75% epiboly whole embryo without xxx sample1 Lane4,2.I1 ep woy 1 Lane4,2.I1 ep woy 1 Lane4,mH2A1 75% epiboly whole embryo without xxx sample1 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,2.I1-ep-woy-1-Lane4-R1.fastq 2.I1-ep-woy-1-Lane4-R2.fastq,fastq fastq,482807769.0,3198461.0,2.I1 ep woy 1 Lane4 R1.fastq,0:75.51 1:75.44,A:137055500;C:104480327;G:106222472;T:134777294;N:272176,75,75,,,137055500,104480327,106222472,134777294,272176,SRX4729608,SRS3812046,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.93786,0.94272,0.09318,0.0899,0.78723,0.78579,0.50212,0.50383,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49350,SRR7891996,SRX4729602,SRS3812038,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP POSITIVE sample1 Lane2,11.I2 24 gfp 1 Lane2,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP POSITIVE sample1 Lane2|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP POSITIVE sample1 Lane2,11.I2 24 gfp 1 Lane2,11.I2 24 gfp 1 Lane2,mH2A2 24hpf GFP POSITIVE sample1 Lane2,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,11.I2-24-gfp-1-Lane2-R1.fastq 11.I2-24-gfp-1-Lane2-R2.fastq,fastq fastq,533952656.0,3539594.0,11.I2 24 gfp 1 Lane2 R2.fastq,0:75.50 1:75.35,A:133349562;C:132030079;G:135590525;T:132679587;N:302903,75,75,,,133349562,132030079,135590525,132679587,302903,SRX4729602,SRS3812038,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97206,0.97321,0.04343,0.04222,0.73064,0.7346,0.48359,0.47752,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49351,SRR7891997,SRX4729601,SRS3812039,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo without xxx sample1 Lane1,4.I1 24woy 1 Lane1,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo without xxx sample1 Lane1|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo without xxx sample1 Lane1,4.I1 24woy 1 Lane1,4.I1 24woy 1 Lane1,mH2A1 24hpf whole embryo without xxx sample1 Lane1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,4.I1-24woy-1-Lane1-R1.fastq 4.I1-24woy-1-Lane1-R2.fastq,fastq fastq,365985116.0,2425332.0,4.I1 24woy 1 Lane1 R2.fastq,0:75.51 1:75.39,A:94402871;C:86149765;G:91276535;T:93954343;N:201602,75,75,,,94402871,86149765,91276535,93954343,201602,SRX4729601,SRS3812039,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96144,0.96089,0.05067,0.04838,0.75866,0.76248,0.48263,0.47115,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-09-22,Pharyngula,Embryo,Whole Organism,All anatomical structures 49352,SRR7891998,SRX4729600,SRS3812037,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo without xxx sample1 Lane2,4.I1 24woy 1 Lane2,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo without xxx sample1 Lane2|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo without xxx sample1 Lane2,4.I1 24woy 1 Lane2,4.I1 24woy 1 Lane2,mH2A1 24hpf whole embryo without xxx sample1 Lane2,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,4.I1-24woy-1-Lane2-R1.fastq 4.I1-24woy-1-Lane2-R2.fastq,fastq fastq,358233544.0,2374001.0,4.I1 24woy 1 Lane2 R2.fastq,0:75.51 1:75.39,A:92583756;C:84360786;G:89163429;T:91927387;N:198186,75,75,,,92583756,84360786,89163429,91927387,198186,SRX4729600,SRS3812037,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96121,0.9633,0.05041,0.04885,0.75779,0.76264,0.48225,0.48109,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49353,SRR7891999,SRX4729599,SRS3812036,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo sample1 Lane3,3.I1 24 wy 1 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo sample1 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo sample1 Lane3,3.I1 24 wy 1 Lane3,3.I1 24 wy 1 Lane3,mH2A1 24hpf whole embryo sample1 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,3.I1-24-wy-1-Lane3-R1.fastq 3.I1-24-wy-1-Lane3-R2.fastq,fastq fastq,516979926.0,3428157.0,3.I1 24 wy 1 Lane3 R2.fastq,0:75.47 1:75.33,A:127659003;C:127185649;G:135897041;T:125925015;N:313218,75,75,,,127659003,127185649,135897041,125925015,313218,SRX4729599,SRS3812036,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96327,0.96499,0.03464,0.03364,0.72287,0.73034,0.45546,0.45107,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49354,SRR7892000,SRX4729598,SRS3812035,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo sample1 Lane4,3.I1 24 wy 1 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo sample1 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo sample1 Lane4,3.I1 24 wy 1 Lane4,3.I1 24 wy 1 Lane4,mH2A1 24hpf whole embryo sample1 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,3.I1-24-wy-1-Lane4-R1.fastq 3.I1-24-wy-1-Lane4-R2.fastq,fastq fastq,498854125.0,3307997.0,3.I1 24 wy 1 Lane4 R1.fastq,0:75.48 1:75.33,A:123535576;C:122825760;G:130481288;T:121724416;N:287085,75,75,,,123535576,122825760,130481288,121724416,287085,SRX4729598,SRS3812035,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96641,0.96538,0.03499,0.03375,0.72186,0.72924,0.45679,0.46075,75,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49357,SRR7892003,SRX4729595,SRS3812032,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo without xxx sample1 Lane3,4.I1 24woy 1 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo without xxx sample1 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo without xxx sample1 Lane3,4.I1 24woy 1 Lane3,4.I1 24woy 1 Lane3,mH2A1 24hpf whole embryo without xxx sample1 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,4.I1-24woy-1-Lane3-R1.fastq 4.I1-24woy-1-Lane3-R2.fastq,fastq fastq,368815699.0,2444072.0,4.I1 24woy 1 Lane3 R1.fastq,0:75.51 1:75.39,A:95148110;C:86838746;G:91957030;T:94651470;N:220343,75,75,,,95148110,86838746,91957030,94651470,220343,SRX4729595,SRS3812032,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96093,0.96035,0.05066,0.04922,0.75838,0.76426,0.48358,0.46552,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49358,SRR7892004,SRX4729594,SRS3812031,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo without xxx sample1 Lane4,4.I1 24woy 1 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo without xxx sample1 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo without xxx sample1 Lane4,4.I1 24woy 1 Lane4,4.I1 24woy 1 Lane4,mH2A1 24hpf whole embryo without xxx sample1 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,4.I1-24woy-1-Lane4-R1.fastq 4.I1-24woy-1-Lane4-R2.fastq,fastq fastq,358824882.0,2377889.0,4.I1 24woy 1 Lane4 R2.fastq,0:75.51 1:75.39,A:92885821;C:84543736;G:88974435;T:92224934;N:195956,75,75,,,92885821,84543736,88974435,92224934,195956,SRX4729594,SRS3812031,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96171,0.96176,0.05041,0.04848,0.75881,0.76432,0.48084,0.48342,75,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49361,SRR7892007,SRX4729591,SRS3812028,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo without xxx sample2 Lane3,8.I1 24woy 2 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo without xxx sample2 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo without xxx sample2 Lane3,8.I1 24woy 2 Lane3,8.I1 24woy 2 Lane3,mH2A1 24hpf whole embryo without xxx sample2 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,8.I1-24woy-2-Lane3-R1.fastq 8.I1-24woy-2-Lane3-R2.fastq,fastq fastq,193680492.0,1282965.0,8.I1 24woy 2 Lane3 R2.fastq,0:75.55 1:75.41,A:48684626;C:46408424;G:51712095;T:46764610;N:110737,75,75,,,48684626,46408424,51712095,46764610,110737,SRX4729591,SRS3812028,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96989,0.9652,0.03082,0.02974,0.7223,0.73594,0.45961,0.45624,76,36,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49363,SRR7892009,SRX4729589,SRS3812026,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP POSITIVE sample2 Lane3,13.I2 24 gfp 2 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP POSITIVE sample2 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP POSITIVE sample2 Lane3,13.I2 24 gfp 2 Lane3,13.I2 24 gfp 2 Lane3,mH2A2 24hpf GFP POSITIVE sample2 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,13.I2-24-gfp-2-Lane3-R1.fastq 13.I2-24-gfp-2-Lane3-R2.fastq,fastq fastq,548668868.0,3635928.0,13.I2 24 gfp 2 Lane3 R1.fastq,0:75.53 1:75.37,A:135186383;C:137733932;G:138529958;T:136895416;N:323179,75,75,,,135186383,137733932,138529958,136895416,323179,SRX4729589,SRS3812026,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97067,0.97194,0.04129,0.04057,0.73334,0.73468,0.48798,0.48821,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49364,SRR7892010,SRX4729588,SRS3812025,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP POSITIVE sample2 Lane4,13.I2 24 gfp 2 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP POSITIVE sample2 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP POSITIVE sample2 Lane4,13.I2 24 gfp 2 Lane4,13.I2 24 gfp 2 Lane4,mH2A2 24hpf GFP POSITIVE sample2 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,13.I2-24-gfp-2-Lane4-R1.fastq 13.I2-24-gfp-2-Lane4-R2.fastq,fastq fastq,531485598.0,3522107.0,13.I2 24 gfp 2 Lane4 R1.fastq,0:75.53 1:75.37,A:131103619;C:133393545;G:133983687;T:132713068;N:291679,75,75,,,131103619,133393545,133983687,132713068,291679,SRX4729588,SRS3812025,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97018,0.97162,0.0403,0.03911,0.73241,0.73513,0.48616,0.48889,75,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49365,SRR7892011,SRX4729587,SRS3812024,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP POSITIVE sample1 Lane1,11.I2 24 gfp 1 Lane1,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP POSITIVE sample1 Lane1|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP POSITIVE sample1 Lane1,11.I2 24 gfp 1 Lane1,11.I2 24 gfp 1 Lane1,mH2A2 24hpf GFP POSITIVE sample1 Lane1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,11.I2-24-gfp-1-Lane1-R2.fastq 11.I2-24-gfp-1-Lane1-R1.fastq,fastq fastq,548058751.0,3633082.0,11.I2 24 gfp 1 Lane1 R2.fastq,0:75.50 1:75.35,A:136746553;C:135478765;G:139285373;T:136234458;N:313602,75,75,,,136746553,135478765,139285373,136234458,313602,SRX4729587,SRS3812024,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97184,0.97388,0.04351,0.04298,0.73172,0.73391,0.47873,0.4724,73,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-09-22,Pharyngula,Embryo,Whole Organism,All anatomical structures 49366,SRR7892012,SRX4729586,SRS3812023,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo without xxx sample2 Lane4,8.I1 24woy 2 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo without xxx sample2 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo without xxx sample2 Lane4,8.I1 24woy 2 Lane4,8.I1 24woy 2 Lane4,mH2A1 24hpf whole embryo without xxx sample2 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,8.I1-24woy-2-Lane4-R2.fastq 8.I1-24woy-2-Lane4-R1.fastq,fastq fastq,187207314.0,1240103.0,8.I1 24woy 2 Lane4 R2.fastq,0:75.55 1:75.41,A:47354843;C:44924212;G:49469199;T:45356043;N:103017,75,75,,,47354843,44924212,49469199,45356043,103017,SRX4729586,SRS3812023,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96969,0.96716,0.032,0.03067,0.72285,0.73671,0.45962,0.46279,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49367,SRR7892013,SRX4729585,SRS3812022,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP Negative sample2 Lane3,15.I2 24 gfpNeg 2 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP Negative sample2 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP Negative sample2 Lane3,15.I2 24 gfpNeg 2 Lane3,15.I2 24 gfpNeg 2 Lane3,mH2A2 24hpf GFP Negative sample2 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,15.I2-24-gfpNeg-2-Lane3-R2.fastq 15.I2-24-gfpNeg-2-Lane3-R1.fastq,fastq fastq,461113930.0,3057541.0,15.I2 24 gfpNeg 2 Lane3 R1.fastq,0:75.47 1:75.34,A:118045296;C:110305628;G:114439796;T:118048212;N:274998,75,75,,,118045296,110305628,114439796,118048212,274998,SRX4729585,SRS3812022,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.89074,0.89425,0.04862,0.04687,0.79314,0.79584,0.47991,0.47623,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49371,SRR7892017,SRX4729581,SRS3812018,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP Negative sample2 Lane2,15.I2 24 gfpNeg 2 Lane2,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP Negative sample2 Lane2|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP Negative sample2 Lane2,15.I2 24 gfpNeg 2 Lane2,15.I2 24 gfpNeg 2 Lane2,mH2A2 24hpf GFP Negative sample2 Lane2,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,15.I2-24-gfpNeg-2-Lane2-R1.fastq 15.I2-24-gfpNeg-2-Lane2-R2.fastq,fastq fastq,446266499.0,2959116.0,15.I2 24 gfpNeg 2 Lane2 R2.fastq,0:75.48 1:75.34,A:114337410;C:106829603;G:110601960;T:114256127;N:241399,75,75,,,114337410,106829603,110601960,114256127,241399,SRX4729581,SRS3812018,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.89287,0.89661,0.04875,0.0475,0.7962,0.79855,0.45545,0.45051,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49372,SRR7892018,SRX4729580,SRS3812017,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP Negative sample1 Lane2,12.I2 24 gfpNeg 1 Lane2,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP Negative sample1 Lane2|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP Negative sample1 Lane2,12.I2 24 gfpNeg 1 Lane2,12.I2 24 gfpNeg 1 Lane2,mH2A2 24hpf GFP Negative sample1 Lane2,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,12.I2-24-gfpNeg-1-Lane2-R1.fastq 12.I2-24-gfpNeg-1-Lane2-R2.fastq,fastq fastq,499797494.0,3313054.0,12.I2 24 gfpNeg 1 Lane2 R1.fastq,0:75.49 1:75.36,A:126920611;C:121609748;G:124517863;T:126473519;N:275753,75,75,,,126920611,121609748,124517863,126473519,275753,SRX4729580,SRS3812017,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97069,0.97469,0.03048,0.02997,0.76562,0.76816,0.55428,0.5557,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49373,SRR7892019,SRX4729579,SRS3812016,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP Negative sample2 Lane1,15.I2 24 gfpNeg 2 Lane1,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP Negative sample2 Lane1|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP Negative sample2 Lane1,15.I2 24 gfpNeg 2 Lane1,15.I2 24 gfpNeg 2 Lane1,mH2A2 24hpf GFP Negative sample2 Lane1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,15.I2-24-gfpNeg-2-Lane1-R1.fastq 15.I2-24-gfpNeg-2-Lane1-R2.fastq,fastq fastq,459325061.0,3045750.0,15.I2 24 gfpNeg 2 Lane1 R2.fastq,0:75.47 1:75.34,A:117572432;C:109833973;G:114052571;T:117614049;N:252036,75,75,,,117572432,109833973,114052571,117614049,252036,SRX4729579,SRS3812016,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.89119,0.89478,0.04839,0.04749,0.79393,0.79659,0.47337,0.44621,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49374,SRR7892020,SRX4729578,SRS3812015,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP Negative sample1 Lane1,12.I2 24 gfpNeg 1 Lane1,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP Negative sample1 Lane1|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP Negative sample1 Lane1,12.I2 24 gfpNeg 1 Lane1,12.I2 24 gfpNeg 1 Lane1,mH2A2 24hpf GFP Negative sample1 Lane1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,12.I2-24-gfpNeg-1-Lane1-R1.fastq 12.I2-24-gfpNeg-1-Lane1-R2.fastq,fastq fastq,509884469.0,3379906.0,12.I2 24 gfpNeg 1 Lane1 R1.fastq,0:75.49 1:75.36,A:129411379;C:124017303;G:127081604;T:129091371;N:282812,75,75,,,129411379,124017303,127081604,129091371,282812,SRX4729578,SRS3812015,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97028,0.9742,0.03085,0.03042,0.76258,0.76477,0.55645,0.55731,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49375,SRR7892021,SRX4729577,SRS3812014,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 75% epiboly whole embryo without xxx sample1 Lane3,2.I1 ep woy 1 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 75% epiboly whole embryo without xxx sample1 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 75% epiboly whole embryo without xxx sample1 Lane3,2.I1 ep woy 1 Lane3,2.I1 ep woy 1 Lane3,mH2A1 75% epiboly whole embryo without xxx sample1 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,2.I1-ep-woy-1-Lane3-R1.fastq 2.I1-ep-woy-1-Lane3-R2.fastq,fastq fastq,498849723.0,3304727.0,2.I1 ep woy 1 Lane3 R2.fastq,0:75.51 1:75.44,A:141398424;C:108002824;G:110024696;T:139121255;N:302524,75,75,,,141398424,108002824,110024696,139121255,302524,SRX4729577,SRS3812014,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.93785,0.94161,0.09249,0.08826,0.78737,0.78821,0.5078,0.50379,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49376,SRR7892022,SRX4729576,SRS3812013,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP POSITIVE sample1 Lane4,11.I2 24 gfp 1 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP POSITIVE sample1 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP POSITIVE sample1 Lane4,11.I2 24 gfp 1 Lane4,11.I2 24 gfp 1 Lane4,mH2A2 24hpf GFP POSITIVE sample1 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,11.I2-24-gfp-1-Lane4-R1.fastq 11.I2-24-gfp-1-Lane4-R2.fastq,fastq fastq,534383866.0,3542370.0,11.I2 24 gfp 1 Lane4 R2.fastq,0:75.50 1:75.35,A:133580118;C:132126897;G:135428790;T:132950404;N:297657,75,75,,,133580118,132126897,135428790,132950404,297657,SRX4729576,SRS3812013,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97204,0.97436,0.04343,0.04315,0.73093,0.73521,0.47234,0.48034,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-09-22,Pharyngula,Embryo,Whole Organism,All anatomical structures 49377,SRR7892023,SRX4729575,SRS3812012,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP Negative sample1 Lane4,12.I2 24 gfpNeg 1 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP Negative sample1 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP Negative sample1 Lane4,12.I2 24 gfpNeg 1 Lane4,12.I2 24 gfpNeg 1 Lane4,mH2A2 24hpf GFP Negative sample1 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,12.I2-24-gfpNeg-1-Lane4-R2.fastq 12.I2-24-gfpNeg-1-Lane4-R1.fastq,fastq fastq,498547943.0,3304723.0,12.I2 24 gfpNeg 1 Lane4 R1.fastq,0:75.49 1:75.37,A:126730459;C:121260984;G:123996551;T:126277799;N:282150,75,75,,,126730459,121260984,123996551,126277799,282150,SRX4729575,SRS3812012,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97012,0.97403,0.03101,0.0303,0.76301,0.76674,0.5495,0.56051,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49378,SRR7892024,SRX4729574,SRS3812011,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP Negative sample1 Lane3,12.I2 24 gfpNeg 1 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP Negative sample1 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP Negative sample1 Lane3,12.I2 24 gfpNeg 1 Lane3,12.I2 24 gfpNeg 1 Lane3,mH2A2 24hpf GFP Negative sample1 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,12.I2-24-gfpNeg-1-Lane3-R1.fastq 12.I2-24-gfpNeg-1-Lane3-R2.fastq,fastq fastq,516593960.0,3424252.0,12.I2 24 gfpNeg 1 Lane3 R2.fastq,0:75.49 1:75.37,A:131144214;C:125668159;G:128758019;T:130722021;N:301547,75,75,,,131144214,125668159,128758019,130722021,301547,SRX4729574,SRS3812011,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97014,0.97455,0.03036,0.02986,0.76368,0.7667,0.54306,0.56109,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49380,SRR7892026,SRX4729572,SRS3812009,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP POSITIVE sample1 Lane3,11.I2 24 gfp 1 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP POSITIVE sample1 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP POSITIVE sample1 Lane3,11.I2 24 gfp 1 Lane3,11.I2 24 gfp 1 Lane3,mH2A2 24hpf GFP POSITIVE sample1 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,11.I2-24-gfp-1-Lane3-R1.fastq 11.I2-24-gfp-1-Lane3-R2.fastq,fastq fastq,551835380.0,3658036.0,11.I2 24 gfp 1 Lane3 R1.fastq,0:75.50 1:75.36,A:137666150;C:136436663;G:140248966;T:137153858;N:329743,75,75,,,137666150,136436663,140248966,137153858,329743,SRX4729572,SRS3812009,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97135,0.97307,0.04332,0.0429,0.73034,0.73357,0.48713,0.4809,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49381,SRR7892027,SRX4729571,SRS3812008,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo without xxx sample2 Lane2,8.I1 24woy 2 Lane2,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo without xxx sample2 Lane2|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo without xxx sample2 Lane2,8.I1 24woy 2 Lane2,8.I1 24woy 2 Lane2,mH2A1 24hpf whole embryo without xxx sample2 Lane2,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,8.I1-24woy-2-Lane2-R2.fastq 8.I1-24woy-2-Lane2-R1.fastq,fastq fastq,187611963.0,1242871.0,8.I1 24woy 2 Lane2 R1.fastq,0:75.55 1:75.40,A:47354784;C:44926465;G:49945473;T:45282887;N:102354,75,75,,,47354784,44926465,49945473,45282887,102354,SRX4729571,SRS3812008,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.9701,0.9654,0.03169,0.03006,0.7219,0.73618,0.45557,0.45964,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-09-22,Pharyngula,Embryo,Whole Organism,All anatomical structures 49382,SRR7892028,SRX4729570,SRS3812007,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo without xxx sample2 Lane1,8.I1 24woy 2 Lane1,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo whitout yolk|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo without xxx sample2 Lane1|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo without xxx sample2 Lane1,8.I1 24woy 2 Lane1,8.I1 24woy 2 Lane1,mH2A1 24hpf whole embryo without xxx sample2 Lane1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,8.I1-24woy-2-Lane1-R1.fastq 8.I1-24woy-2-Lane1-R2.fastq,fastq fastq,192147411.0,1272836.0,8.I1 24woy 2 Lane1 R2.fastq,0:75.55 1:75.41,A:48219836;C:46036720;G:51357015;T:46430460;N:103380,75,75,,,48219836,46036720,51357015,46430460,103380,SRX4729570,SRS3812007,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.96943,0.96455,0.03082,0.02978,0.72281,0.73547,0.45834,0.45962,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49383,SRR7892029,SRX4729569,SRS3812006,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP POSITIVE sample2 Lane2,13.I2 24 gfp 2 Lane2,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP POSITIVE sample2 Lane2|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP POSITIVE sample2 Lane2,13.I2 24 gfp 2 Lane2,13.I2 24 gfp 2 Lane2,mH2A2 24hpf GFP POSITIVE sample2 Lane2,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,13.I2-24-gfp-2-Lane2-R1.fastq 13.I2-24-gfp-2-Lane2-R2.fastq,fastq fastq,530856186.0,3517946.0,13.I2 24 gfp 2 Lane2 R1.fastq,0:75.53 1:75.37,A:130853185;C:133292358;G:133981643;T:132436018;N:292982,75,75,,,130853185,133292358,133981643,132436018,292982,SRX4729569,SRS3812006,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97045,0.97167,0.03936,0.03918,0.73306,0.73588,0.48404,0.49129,76,74,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49384,SRR7892030,SRX4729568,SRS3812004,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A2 24hpf GFP POSITIVE sample2 Lane1,13.I2 24 gfp 2 Lane1,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo without xxx|genotype:TgmH2A2:GFP mH2A2.|samples information:mH2A2 24hpf GFP POSITIVE sample2 Lane1|BioSampleModel:Model organism or animal,,,,,,,,,mH2A2 24hpf GFP POSITIVE sample2 Lane1,13.I2 24 gfp 2 Lane1,13.I2 24 gfp 2 Lane1,mH2A2 24hpf GFP POSITIVE sample2 Lane1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,13.I2-24-gfp-2-Lane1-R1.fastq 13.I2-24-gfp-2-Lane1-R2.fastq,fastq fastq,544622375.0,3609220.0,13.I2 24 gfp 2 Lane1 R1.fastq,0:75.53 1:75.37,A:134206994;C:136690485;G:137477997;T:135946996;N:299903,75,75,,,134206994,136690485,137477997,135946996,299903,SRX4729568,SRS3812004,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97144,0.97156,0.04016,0.0392,0.73419,0.73726,0.48244,0.47683,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49389,SRR7892035,SRX4729563,SRS3812001,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo sample2 Lane4,7.I1 24 wy 2 Lane4,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo sample2 Lane4|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo sample2 Lane4,7.I1 24 wy 2 Lane4,7.I1 24 wy 2 Lane4,mH2A1 24hpf whole embryo sample2 Lane4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,7.I1-24-wy-2-Lane4-R1.fastq 7.I1-24-wy-2-Lane4-R2.fastq,fastq fastq,294210344.0,1950249.0,7.I1 24 wy 2 Lane4 R1.fastq,0:75.50 1:75.36,A:73291672;C:71932032;G:75879308;T:72936427;N:170905,75,75,,,73291672,71932032,75879308,72936427,170905,SRX4729563,SRS3812001,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97114,0.96967,0.03569,0.03491,0.72072,0.72841,0.45568,0.46774,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49390,SRR7892036,SRX4729562,SRS3812041,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo sample2 Lane3,7.I1 24 wy 2 Lane3,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo sample2 Lane3|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo sample2 Lane3,7.I1 24 wy 2 Lane3,7.I1 24 wy 2 Lane3,mH2A1 24hpf whole embryo sample2 Lane3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,7.I1-24-wy-2-Lane3-R1.fastq 7.I1-24-wy-2-Lane3-R2.fastq,fastq fastq,304401439.0,2017775.0,7.I1 24 wy 2 Lane3 R2.fastq,0:75.50 1:75.36,A:75623564;C:74364446;G:78891710;T:75334292;N:187427,75,75,,,75623564,74364446,78891710,75334292,187427,SRX4729562,SRS3812041,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97142,0.96989,0.03526,0.03391,0.72212,0.72878,0.45861,0.46695,76,35,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49391,SRR7892037,SRX4729561,SRS3811999,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo sample2 Lane2,7.I1 24 wy 2 Lane2,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo sample2 Lane2|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo sample2 Lane2,7.I1 24 wy 2 Lane2,7.I1 24 wy 2 Lane2,mH2A1 24hpf whole embryo sample2 Lane2,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,7.I1-24-wy-2-Lane2-R1.fastq 7.I1-24-wy-2-Lane2-R2.fastq,fastq fastq,294800482.0,1954216.0,7.I1 24 wy 2 Lane2 R1.fastq,0:75.50 1:75.35,A:73364327;C:72024312;G:76284297;T:72963369;N:164177,75,75,,,73364327,72024312,76284297,72963369,164177,SRX4729561,SRS3811999,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97127,0.96921,0.03613,0.03539,0.72245,0.72934,0.45364,0.46819,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 49392,SRR7892038,SRX4729560,SRS3812000,SRP162371,PRJNA492713,Zebrafish macroH2A variants analysis reveals distinct embryo localization and function RNASeq Information,PRJNA492713,Other,Most mouse and cell based studies have shown that macroH2A histone variants predominantly associate with heterochromatin and have been associated with gene repression and with an important function in cell differentiation and inhibiting acquisition of pluripotency of pluripotency. However fewer studies have analysed the role of macroH2A during early embryo development. In the project transgenic zebrafish lines were developed expressing macroH2A isoforms mH2A1 and mH2A2 fusion proteins GFP under endogenous identified promoters to study their function during embryogenesis.,,,,mH2A1 24hpf whole embryo sample2 Lane1,7.I1 24 wy 2 Lane1,,strain:TAB.L ABxTL|dev stage:24hpf|sex:pooled male and female|tissue:whole embryo|genotype:Tg mH2A1:GFP mH2A1|samples information:mH2A1 24hpf whole embryo sample2 Lane1|BioSampleModel:Model organism or animal,,,,,,,,,mH2A1 24hpf whole embryo sample2 Lane1,7.I1 24 wy 2 Lane1,7.I1 24 wy 2 Lane1,mH2A1 24hpf whole embryo sample2 Lane1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP162371,,,7.I1-24-wy-2-Lane1-R1.fastq 7.I1-24-wy-2-Lane1-R2.fastq,fastq fastq,301440787.0,1998238.0,7.I1 24 wy 2 Lane1 R1.fastq,0:75.50 1:75.35,A:74863585;C:73624293;G:78143440;T:74638527;N:170942,75,75,,,74863585,73624293,78143440,74638527,170942,SRX4729560,SRS3812000,SRA782245,University of Nebraska Lincoln|Electrical and Computer Engineering,University of Nebraska Lincoln,2,0.97035,0.96906,0.03608,0.03501,0.72218,0.72809,0.45366,0.46926,76,74,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-10-21,Pharyngula,Embryo,Whole Organism,All anatomical structures 55866,SRR10863008,SRX7533061,SRS5972270,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt PGCs 1dpf rep4,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: PGCs 1dpf,wt PGCs 1dpf S1,wt PGCs 1dpf S1,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP241074,,,wt_PGCs_1dpf_S1.R1.fastq.gz,fastq,6787337699.0,81775153.0,wt PGCs 1dpf S1.R1.fastq.gz,0:83 1:0,A:1839754910;C:1566044514;G:1538211923;T:1843241243;N:85109,83,0,,,1839754910,1566044514,1538211923,1843241243,85109,SRX7533061,SRS5972270,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.94441,,0.056,,0.68866,,0.47945,,83,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 55880,SRR10863022,SRX7533047,SRS5972268,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt PGCs 1dpf rep3,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: PGCs 1dpf,imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3,imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_03_20_1dpf_PGCs_rep3_S3.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_03_20_1dpf_PGCs_rep3_S3.R2.fastq.gz,fastq fastq,3406105382.0,21557629.0,imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3.R1.fastq.gz,0:79 1:79,A:914561772;C:790081165;G:768217890;T:933018206;N:226349,79,79,,,914561772,790081165,768217890,933018206,226349,SRX7533047,SRS5972268,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.93859,0.93927,0.06346,0.06362,0.68467,0.68665,0.51016,0.44765,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 55881,SRR10863023,SRX7533046,SRS5972267,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt PGCs 1dpf rep2,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: PGCs 1dpf,imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2,imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_02_30_1dpf_PGCs_rep2_S2.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_02_30_1dpf_PGCs_rep2_S2.R2.fastq.gz,fastq fastq,3126220074.0,19786203.0,imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2.R1.fastq.gz,0:79 1:79,A:835660285;C:727271703;G:711392935;T:851683391;N:211760,79,79,,,835660285,727271703,711392935,851683391,211760,SRX7533046,SRS5972267,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.93836,0.93845,0.05796,0.0579,0.67805,0.68002,0.49555,0.49733,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 55885,SRR10863024,SRX7533042,SRS5972265,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt PGCs 1dpf rep1,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: PGCs 1dpf,imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1,imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_01_24_1dpf_PGCs_rep1_S1.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_01_24_1dpf_PGCs_rep1_S1.R2.fastq.gz,fastq fastq,3512354852.0,22230094.0,imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1.R1.fastq.gz,0:79 1:79,A:937439392;C:820724988;G:797835842;T:956108725;N:245905,79,79,,,937439392,820724988,797835842,956108725,245905,SRX7533042,SRS5972265,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.94053,0.94062,0.05733,0.05792,0.6801,0.68174,0.49423,0.49408,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 55895,SRR10863036,SRX7533032,SRS5972257,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt Fish 1dpf rep2,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: Fish 1dpf,imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14,imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_14_69_1dpf_Fish_rep2_S14.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_14_69_1dpf_Fish_rep2_S14.R2.fastq.gz,fastq fastq,3173577572.0,20085934.0,imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14.R1.fastq.gz,0:79 1:79,A:851665093;C:736131084;G:718748661;T:866816699;N:216035,79,79,,,851665093,736131084,718748661,866816699,216035,SRX7533032,SRS5972257,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.94469,0.9439,0.08631,0.08612,0.71062,0.71204,0.46629,0.46237,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 55896,SRR10863037,SRX7533031,SRS5972256,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.,,wt Fish 1dpf rep1,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: Fish 1dpf,imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13,imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_13_01_1dpf_Fish_rep1_S13.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_13_01_1dpf_Fish_rep1_S13.R2.fastq.gz,fastq fastq,3241792492.0,20517674.0,imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13.R1.fastq.gz,0:79 1:79,A:865936682;C:756362974;G:735614291;T:883655547;N:222998,79,79,,,865936682,756362974,735614291,883655547,222998,SRX7533031,SRS5972256,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.94544,0.94715,0.08154,0.0819,0.70928,0.71011,0.45932,0.46165,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 61824,SRR12998953,SRX9450376,SRS7663343,SRP291417,PRJNA675020,The genome wide impact of nipblb loss of function on zebrafish gene expression,PRJNA675020,Other,Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity such as the cohesin genes and their regulator NIPBL. In our previous studies using a zebrafish model for nipblb knock down we described the effect of nipblb loss of function in specific contexts such as central nervous system development and hematopoiesis. However the genome wide transcriptional impact of nipblb loss of function in zebrafish embryos at diverse developmental stages remains under investigated. By RNA seq analyses in zebrafish embryos at 24 hpf we examined genome wide effects of nipblb haploinsufficiency on transcriptional programs. Differential gene expression analysis revealed that nipblb loss of function has a major impact on gene expression at 24 hpf and that this massive transcriptional dysregulation is rescued by specific back up mechanisms that counteract the transcriptional patterns induced by nipblb silencing. Moreover we unraveled a connection between nipblb dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes enforcing our previous evidences on the involvement of NIPBL related transcriptional dysregulation in hematological malignancies.,,,total RNA from zebrafish embryos,,Nipblb 24h 3,,strain:AB|age:24 hpf stage:embryo|sex:not determined|tissue:embryos|biomaterial provider:Prof. Anna Pistocchi Dept. of Medical Biotechnology and Translational Medicine University of Milan|replicate:3|genotype:mutated|sample type:whole organism|store cond:immediate extration|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio Nipblb MO mutated at 24 hpf replicate 3,Illumina Nipblb 24h 3,Illumina Nipblb 24h 3,RNA extracted from nipblb MO embryos at 24 hpf were used to prepare Illumina TruSeq Stranded mRNA Library then sequenced on Illumina HiSeq 4000 platform by paired end run,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291417,,,Nipblb_24h_3_R1.fastq.gz Nipblb_24h_3_R2.fastq.gz,fastq fastq,8181438210.0,27090855.0,Nipblb 24h 3 R1.fastq.gz,0:151 1:151,A:2132944325;C:1957634133;G:2049091890;T:2041642294;N:125568,151,151,,,2132944325,1957634133,2049091890,2041642294,125568,SRX9450376,SRS7663343,SRA1155106,National Research Council (CNR)|Institute of Biomedical Technologies,"National Research Council (CNR) Prof. Anna Pistocchi, Dept. of Medical Biotechnology and Translational Medicine -University of Milan",2,0.95635,0.95634,0.04249,0.04194,0.71114,0.71463,0.46258,0.46355,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Italy,2020-11-06,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 61825,SRR12998954,SRX9450375,SRS7663342,SRP291417,PRJNA675020,The genome wide impact of nipblb loss of function on zebrafish gene expression,PRJNA675020,Other,Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity such as the cohesin genes and their regulator NIPBL. In our previous studies using a zebrafish model for nipblb knock down we described the effect of nipblb loss of function in specific contexts such as central nervous system development and hematopoiesis. However the genome wide transcriptional impact of nipblb loss of function in zebrafish embryos at diverse developmental stages remains under investigated. By RNA seq analyses in zebrafish embryos at 24 hpf we examined genome wide effects of nipblb haploinsufficiency on transcriptional programs. Differential gene expression analysis revealed that nipblb loss of function has a major impact on gene expression at 24 hpf and that this massive transcriptional dysregulation is rescued by specific back up mechanisms that counteract the transcriptional patterns induced by nipblb silencing. Moreover we unraveled a connection between nipblb dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes enforcing our previous evidences on the involvement of NIPBL related transcriptional dysregulation in hematological malignancies.,,,total RNA from zebrafish embryos,,Nipblb 24h 2,,strain:AB|age:24 hpf stage:embryo|sex:not determined|tissue:embryos|biomaterial provider:Prof. Anna Pistocchi Dept. of Medical Biotechnology and Translational Medicine University of Milan|replicate:2|genotype:mutated|sample type:whole organism|store cond:immediate extration|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio Nipblb MO mutated at 24 hpf replicate 2,Illumina Nipblb 24h 2,Illumina Nipblb 24h 2,RNA extracted from nipblb MO embryos at 24 hpf were used to prepare Illumina TruSeq Stranded mRNA Library then sequenced on Illumina HiSeq 4000 platform by paired end run,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291417,,,Nipblb_24h_2_R1.fastq.gz Nipblb_24h_2_R2.fastq.gz,fastq fastq,12849588714.0,42548307.0,Nipblb 24h 2 R1.fastq.gz,0:151 1:151,A:3338078330;C:3079930308;G:3247195790;T:3184188818;N:195468,151,151,,,3338078330,3079930308,3247195790,3184188818,195468,SRX9450375,SRS7663342,SRA1155106,National Research Council (CNR)|Institute of Biomedical Technologies,"National Research Council (CNR) Prof. Anna Pistocchi, Dept. of Medical Biotechnology and Translational Medicine -University of Milan",2,0.95823,0.95812,0.04147,0.04104,0.71108,0.71386,0.47215,0.4694,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Italy,2020-11-06,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 61826,SRR12998955,SRX9450374,SRS7663341,SRP291417,PRJNA675020,The genome wide impact of nipblb loss of function on zebrafish gene expression,PRJNA675020,Other,Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity such as the cohesin genes and their regulator NIPBL. In our previous studies using a zebrafish model for nipblb knock down we described the effect of nipblb loss of function in specific contexts such as central nervous system development and hematopoiesis. However the genome wide transcriptional impact of nipblb loss of function in zebrafish embryos at diverse developmental stages remains under investigated. By RNA seq analyses in zebrafish embryos at 24 hpf we examined genome wide effects of nipblb haploinsufficiency on transcriptional programs. Differential gene expression analysis revealed that nipblb loss of function has a major impact on gene expression at 24 hpf and that this massive transcriptional dysregulation is rescued by specific back up mechanisms that counteract the transcriptional patterns induced by nipblb silencing. Moreover we unraveled a connection between nipblb dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes enforcing our previous evidences on the involvement of NIPBL related transcriptional dysregulation in hematological malignancies.,,,total RNA from zebrafish embryos,,Nipblb 24h 1,,strain:AB|age:24 hpf stage:embryo|sex:not determined|tissue:embryos|biomaterial provider:Prof. Anna Pistocchi Dept. of Medical Biotechnology and Translational Medicine University of Milan|replicate:1|genotype:mutated|sample type:whole organism|store cond:immediate extration|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio Nipblb MO mutated at 24 hpf replicate 1,Illumina Nipblb 24h 1,Illumina Nipblb 24h 1,RNA extracted from nipblb MO embryos at 24 hpf were used to prepare Illumina TruSeq Stranded mRNA Library then sequenced on Illumina HiSeq 4000 platform by paired end run,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291417,,,Nipblb_24h_1_R1.fastq.gz Nipblb_24h_1_R2.fastq.gz,fastq fastq,10997889606.0,36416853.0,Nipblb 24h 1 R1.fastq.gz,0:151 1:151,A:2901814647;C:2598572158;G:2704147610;T:2793193400;N:161791,151,151,,,2901814647,2598572158,2704147610,2793193400,161791,SRX9450374,SRS7663341,SRA1155106,National Research Council (CNR)|Institute of Biomedical Technologies,"National Research Council (CNR) Prof. Anna Pistocchi, Dept. of Medical Biotechnology and Translational Medicine -University of Milan",2,0.95506,0.9539,0.05267,0.05169,0.70954,0.7139,0.47629,0.47367,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Italy,2020-11-06,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 61827,SRR12998959,SRX9450370,SRS7663337,SRP291417,PRJNA675020,The genome wide impact of nipblb loss of function on zebrafish gene expression,PRJNA675020,Other,Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity such as the cohesin genes and their regulator NIPBL. In our previous studies using a zebrafish model for nipblb knock down we described the effect of nipblb loss of function in specific contexts such as central nervous system development and hematopoiesis. However the genome wide transcriptional impact of nipblb loss of function in zebrafish embryos at diverse developmental stages remains under investigated. By RNA seq analyses in zebrafish embryos at 24 hpf we examined genome wide effects of nipblb haploinsufficiency on transcriptional programs. Differential gene expression analysis revealed that nipblb loss of function has a major impact on gene expression at 24 hpf and that this massive transcriptional dysregulation is rescued by specific back up mechanisms that counteract the transcriptional patterns induced by nipblb silencing. Moreover we unraveled a connection between nipblb dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes enforcing our previous evidences on the involvement of NIPBL related transcriptional dysregulation in hematological malignancies.,,,total RNA from zebrafish embryos,,CTRL 24h 3,,strain:AB|age:24 hpf stage:embryo|sex:not determined|tissue:embryos|biomaterial provider:Prof. Anna Pistocchi Dept. of Medical Biotechnology and Translational Medicine University of Milan|replicate:3|genotype:wild type|sample type:whole organism|store cond:immediate extration|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio control MO wild type at 24 hpf replicate 3,Illumina CTRL 24h 3,Illumina CTRL 24h 3,RNA extracted from ctrl MO embryos at 24 hpf were used to prepare Illumina TruSeq Stranded mRNA Library then sequenced on Illumina HiSeq 4000 platform by paired end run,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291417,,,CTRL_24h_3_R1.fastq.gz CTRL_24h_3_R2.fastq.gz,fastq fastq,11743125342.0,38884521.0,CTRL 24h 3 R1.fastq.gz,0:151 1:151,A:3020506340;C:2830362106;G:2947603520;T:2944481126;N:172250,151,151,,,3020506340,2830362106,2947603520,2944481126,172250,SRX9450370,SRS7663337,SRA1155106,National Research Council (CNR)|Institute of Biomedical Technologies,"National Research Council (CNR) Prof. Anna Pistocchi, Dept. of Medical Biotechnology and Translational Medicine -University of Milan",2,0.95692,0.95604,0.05664,0.05614,0.67375,0.6786,0.4617,0.45912,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Italy,2020-11-06,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 61828,SRR12998962,SRX9450367,SRS7663334,SRP291417,PRJNA675020,The genome wide impact of nipblb loss of function on zebrafish gene expression,PRJNA675020,Other,Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity such as the cohesin genes and their regulator NIPBL. In our previous studies using a zebrafish model for nipblb knock down we described the effect of nipblb loss of function in specific contexts such as central nervous system development and hematopoiesis. However the genome wide transcriptional impact of nipblb loss of function in zebrafish embryos at diverse developmental stages remains under investigated. By RNA seq analyses in zebrafish embryos at 24 hpf we examined genome wide effects of nipblb haploinsufficiency on transcriptional programs. Differential gene expression analysis revealed that nipblb loss of function has a major impact on gene expression at 24 hpf and that this massive transcriptional dysregulation is rescued by specific back up mechanisms that counteract the transcriptional patterns induced by nipblb silencing. Moreover we unraveled a connection between nipblb dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes enforcing our previous evidences on the involvement of NIPBL related transcriptional dysregulation in hematological malignancies.,,,total RNA from zebrafish embryos,,CTRL 24h 2,,strain:AB|age:24 hpf stage:embryo|sex:not determined|tissue:embryos|biomaterial provider:Prof. Anna Pistocchi Dept. of Medical Biotechnology and Translational Medicine University of Milan|replicate:2|genotype:wild type|sample type:whole organism|store cond:immediate extration|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio control MO wild type at 24 hpf replicate 2,Illumina CTRL 24h 2,Illumina CTRL 24h 2,RNA extracted from ctrl MO embryos at 24 hpf were used to prepare Illumina TruSeq Stranded mRNA Library then sequenced on Illumina HiSeq 4000 platform by paired end run,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291417,,,CTRL_24h_2_R1.fastq.gz CTRL_24h_2_R2.fastq.gz,fastq fastq,12249006146.0,40559623.0,CTRL 24h 2 R1.fastq.gz,0:151 1:151,A:3182596147;C:2937226102;G:3070822194;T:3058177433;N:184270,151,151,,,3182596147,2937226102,3070822194,3058177433,184270,SRX9450367,SRS7663334,SRA1155106,National Research Council (CNR)|Institute of Biomedical Technologies,"National Research Council (CNR) Prof. Anna Pistocchi, Dept. of Medical Biotechnology and Translational Medicine -University of Milan",2,0.95517,0.95635,0.05877,0.05793,0.67687,0.67976,0.44921,0.45064,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Italy,2020-11-06,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 61829,SRR12998963,SRX9450366,SRS7663333,SRP291417,PRJNA675020,The genome wide impact of nipblb loss of function on zebrafish gene expression,PRJNA675020,Other,Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity such as the cohesin genes and their regulator NIPBL. In our previous studies using a zebrafish model for nipblb knock down we described the effect of nipblb loss of function in specific contexts such as central nervous system development and hematopoiesis. However the genome wide transcriptional impact of nipblb loss of function in zebrafish embryos at diverse developmental stages remains under investigated. By RNA seq analyses in zebrafish embryos at 24 hpf we examined genome wide effects of nipblb haploinsufficiency on transcriptional programs. Differential gene expression analysis revealed that nipblb loss of function has a major impact on gene expression at 24 hpf and that this massive transcriptional dysregulation is rescued by specific back up mechanisms that counteract the transcriptional patterns induced by nipblb silencing. Moreover we unraveled a connection between nipblb dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes enforcing our previous evidences on the involvement of NIPBL related transcriptional dysregulation in hematological malignancies.,,,total RNA from zebrafish embryos,,CTRL 24h 1,,strain:AB|age:24 hpf stage:embryo|sex:not determined|tissue:embryos|biomaterial provider:Prof. Anna Pistocchi Dept. of Medical Biotechnology and Translational Medicine University of Milan|replicate:1|genotype:wild type|sample type:whole organism|store cond:immediate extration|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio control MO wild type at 24 hpf replicate 1,Illumina CTRL 24h 1,Illumina CTRL 24h 1,RNA extracted from ctrl MO embryos at 24 hpf were used to prepare Illumina TruSeq Stranded mRNA Library then sequenced on Illumina HiSeq 4000 platform by paired end run,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291417,,,CTRL_24h_1_R1.fastq.gz CTRL_24h_1_R2.fastq.gz,fastq fastq,15075335358.0,49918329.0,CTRL 24h 1 R1.fastq.gz,0:151 1:151,A:3961053626;C:3558857892;G:3704787969;T:3850418311;N:217560,151,151,,,3961053626,3558857892,3704787969,3850418311,217560,SRX9450366,SRS7663333,SRA1155106,National Research Council (CNR)|Institute of Biomedical Technologies,"National Research Council (CNR) Prof. Anna Pistocchi, Dept. of Medical Biotechnology and Translational Medicine -University of Milan",2,0.95337,0.95326,0.06617,0.06479,0.67312,0.67596,0.46164,0.46562,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Italy,2020-11-06,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures