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81 rows where devstage_curation = "Pharyngula" and experiment.library_selection = "PolyA"

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tissue_curation 3

tissue_curation_coarse 2

technology 2

experiment.platform 2

experiment.library_strategy 2

experiment.library_layout 2

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 81 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Pharyngula · 81 ✖
Link 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
306 306 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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
307 307 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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
308 308 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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
309 309 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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
310 310 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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
311 311 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>91</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>91</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;