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21 rows where experiment.library_selection = "PolyA", technology = "unknown" and tissue_curation = "Multi-tissue"

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devstage_curation_coarse 3

devstage_curation 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 21 ✖

technology 1

  • unknown · 21 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 21 ✖
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
175 175 DRR084197 DRX078028 DRS086522 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     natural paring early sample zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2] SAMD00073604   sample name:M 4th|replicate:biological replicate 2                 Illumina HiSeq 2500 sequencing of SAMD00073604 DRX078028 zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073604       1389837888.0 38606608.0 DRR084197 0:36 A:320671418;C:336948866;G:347550258;T:381720581;N:2946765 36       320671418 336948866 347550258 381720581 2946765 DRX078028 DRS086522 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.89763   0.02235   0.76445   0.46381   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Zygote Embryo Multi-tissue Multi-system
181 181 DRR084191 DRX078022 DRS086516 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     natural paring early sample zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1] SAMD00073598   sample name:M|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073598 DRX078022 zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073598       1050981012.0 29193917.0 DRR084191 0:36 A:241048832;C:256186268;G:260277071;T:293299597;N:169244 36       241048832 256186268 260277071 293299597 169244 DRX078022 DRS086516 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.9088   0.02369   0.7624   0.47998   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Zygote Embryo Multi-tissue Multi-system
10147 10147 ERR5005147 ERX4814430 ERS5474667 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. 6wpf rep2 RNA SAMEA7727294 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727294|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:6wpf rep2 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:6wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:6wpf rep2 RNA p 6wpf rep2 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 6wpf_rep2_RNA_R1.fastq.gz 6wpf_rep2_RNA_R2.fastq.gz fastq fastq 11929324428.0 40157012.0 E MTAB 9924:6wpf rep2 RNA R 0:148.72 1:148.34 A:3237937670;C:2713313024;G:2724528618;T:3251908184;N:1636932 148 148     3237937670 2713313024 2724528618 3251908184 1636932 ERX4814430 ERS5474667 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.93069 0.93326 0.13891 0.13708 0.69779 0.71701 0.49797 0.49993 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Larval Larval Multi-tissue Multi-system
10148 10148 ERR5005146 ERX4814429 ERS5474666 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. 6wpf rep1 RNA SAMEA7727293 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727293|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:6wpf rep1 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:6wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:6wpf rep1 RNA p 6wpf rep1 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 6wpf_rep1_RNA_R1.fastq.gz 6wpf_rep1_RNA_R2.fastq.gz fastq fastq 19633084666.0 66362913.0 E MTAB 9924:6wpf rep1 RNA R 0:148.10 1:147.74 A:5348913370;C:4443593237;G:4456508875;T:5380825384;N:3243800 148 147     5348913370 4443593237 4456508875 5380825384 3243800 ERX4814429 ERS5474666 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.92182 0.92338 0.12138 0.11866 0.68499 0.70236 0.50638 0.51742 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Larval Larval Multi-tissue Multi-system
10149 10149 ERR5005145 ERX4814428 ERS5474665 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. adult rep2 RNA SAMEA7727292 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727292|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:adult rep2 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:adult rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:adult rep2 RNA p adult rep2 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 adult_rep2_RNA_R1.fastq.gz adult_rep2_RNA_R2.fastq.gz fastq fastq 15648506033.0 52770962.0 E MTAB 9924:adult rep2 RNA R 0:148.45 1:148.09 A:4268818428;C:3540462921;G:3548332979;T:4288409679;N:2482026 148 148     4268818428 3540462921 3548332979 4288409679 2482026 ERX4814428 ERS5474665 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.94625 0.94771 0.13596 0.1321 0.691 0.70709 0.53016 0.5357 148 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Adult Adult Multi-tissue Multi-system
10150 10150 ERR5005144 ERX4814427 ERS5474664 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. adult rep1 RNA SAMEA7727291 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727291|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:adult rep1 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:adult rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:adult rep1 RNA p adult rep1 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 adult_rep1_RNA_R1.fastq.gz adult_rep1_RNA_R2.fastq.gz fastq fastq 12526662412.0 42363955.0 E MTAB 9924:adult rep1 RNA R 0:148.02 1:147.67 A:3489175783;C:2756879350;G:2771544913;T:3507538808;N:1523558 148 147     3489175783 2756879350 2771544913 3507538808 1523558 ERX4814427 ERS5474664 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.94246 0.94448 0.14788 0.14431 0.70065 0.7181 0.50361 0.50894 149 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Adult Adult Multi-tissue Multi-system
10151 10151 ERR5005143 ERX4814426 ERS5474663 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. 4wpf rep2 RNA SAMEA7727290 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727290|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:4wpf rep2 RNA|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:4wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:4wpf rep2 RNA p 4wpf rep2 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:4|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 4wpf_rep2_RNA_R1.fastq.gz 4wpf_rep2_RNA_R2.fastq.gz fastq fastq 17862998816.0 62733750.0 E MTAB 9924:4wpf rep2 RNA R 0:142.46 1:142.28 A:4963776868;C:3947656384;G:3887833339;T:5057912943;N:5819282 142 142     4963776868 3947656384 3887833339 5057912943 5819282 ERX4814426 ERS5474663 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.9309 0.93111 0.1952 0.1951 0.70534 0.7176 0.50482 0.51152 116 147 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Larval Larval Multi-tissue Multi-system
10152 10152 ERR5005142 ERX4814425 ERS5474662 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. 4wpf rep1 RNA SAMEA7727289 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727289|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:4wpf rep1 RNA|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:4wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:4wpf rep1 RNA p 4wpf rep1 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:4|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 4wpf_rep1_RNA_R1.fastq.gz 4wpf_rep1_RNA_R2.fastq.gz fastq fastq 17991275539.0 62100394.0 E MTAB 9924:4wpf rep1 RNA R 0:144.97 1:144.75 A:5021314085;C:3954412393;G:3881029269;T:5128240171;N:6279621 144 144     5021314085 3954412393 3881029269 5128240171 6279621 ERX4814425 ERS5474662 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.92732 0.92708 0.18879 0.18795 0.70171 0.71634 0.506 0.50887 150 149 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Larval Larval Multi-tissue Multi-system
10153 10153 ERR5005141 ERX4814424 ERS5474661 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. 3wpf rep2 RNA SAMEA7727288 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727288|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:3wpf rep2 RNA|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:3wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:3wpf rep2 RNA p 3wpf rep2 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:3|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 3wpf_rep2_RNA_R1.fastq.gz 3wpf_rep2_RNA_R2.fastq.gz fastq fastq 22804042203.0 76957632.0 E MTAB 9924:3wpf rep2 RNA R 0:148.34 1:147.98 A:6255991654;C:5120232312;G:5136799470;T:6288581486;N:2437281 148 147     6255991654 5120232312 5136799470 6288581486 2437281 ERX4814424 ERS5474661 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.93211 0.93322 0.20907 0.2056 0.6983 0.71652 0.53448 0.5352 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Larval Larval Multi-tissue Multi-system
10154 10154 ERR5005140 ERX4814423 ERS5474660 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. 3wpf rep1 RNA SAMEA7727287 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727287|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:3wpf rep1 RNA|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:3wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:3wpf rep1 RNA p 3wpf rep1 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:3|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 3wpf_rep1_RNA_R1.fastq.gz 3wpf_rep1_RNA_R2.fastq.gz fastq fastq 25549987003.0 86260528.0 E MTAB 9924:3wpf rep1 RNA R 0:148.28 1:147.91 A:6961927451;C:5786809647;G:5798882444;T:6999483818;N:2883643 148 147     6961927451 5786809647 5798882444 6999483818 2883643 ERX4814423 ERS5474660 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.93267 0.93467 0.20372 0.20263 0.69252 0.70962 0.53426 0.54087 149 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Larval Larval Multi-tissue Multi-system
28882 28882 SRR26783947 SRX22482174 SRS19495555 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         Non leukemic kidney marrow control #2   isolate:UAS::GFP control #2|age:9 month 16 month|collection date:2023 01 12|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: non leukemic whole kidney marrow #2 A10 A10 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A10_EKRN230034972-1A_HHG75DSX7_L2_2.fq.gz A10_EKRN230034972-1A_HHG75DSX7_L2_1.fq.gz fastq fastq 7982890500.0 26609635.0 A10 EKRN230034972 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:2129699297;C:1884782648;G:1870728993;T:2097648646;N:30916 150 150     2129699297 1884782648 1870728993 2097648646 30916 SRX22482174 SRS19495555 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.93382 0.93397 0.06505 0.06535 0.69826 0.69875 0.51693 0.51829 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28883 28883 SRR26783948 SRX22482173 SRS19495553 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         Non leukemic kidney marrow control #1   isolate:UAS::GFP control #1|age:9 month 16 month|collection date:2023 01 11|geo loc name:Finland: Tampere Europe|sex:male|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: non leukemic whole kidney marrow #1 A9 A9 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A9_EKRN230034971-1A_HHG75DSX7_L2_1.fq.gz A9_EKRN230034971-1A_HHG75DSX7_L2_2.fq.gz fastq fastq 6119764500.0 20399215.0 A9 EKRN230034971 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:1652919782;C:1426521039;G:1415190390;T:1625109104;N:24185 150 150     1652919782 1426521039 1415190390 1625109104 24185 SRX22482173 SRS19495553 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.93503 0.93495 0.07197 0.07148 0.71995 0.71973 0.5119 0.51499 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28884 28884 SRR26783949 SRX22482172 SRS19495554 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         ETV6::RUNX1 tumor #8   isolate:ETV6::RUNX1 knock in zebrafish #8|age:9 month 16 month|collection date:2023 05 10|geo loc name:Finland: Tampere Europe|sex:male|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: leukemic whole kidney marrow #8 A8 A8 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A8_EKRN230034970-1A_HHG75DSX7_L2_1.fq.gz A8_EKRN230034970-1A_HHG75DSX7_L2_2.fq.gz fastq fastq 7920658200.0 26402194.0 A8 EKRN230034970 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:2084803636;C:1894755310;G:1880741705;T:2060327167;N:30382 150 150     2084803636 1894755310 1880741705 2060327167 30382 SRX22482172 SRS19495554 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.93929 0.94055 0.10937 0.1102 0.71741 0.71756 0.46004 0.46358 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28885 28885 SRR26783950 SRX22482171 SRS19495552 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         ETV6::RUNX1 tumor #7   isolate:ETV6::RUNX1 knock in zebrafish #7|age:9 month 16 month|collection date:2023 03 09|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: leukemic whole kidney marrow #7 A7 A7 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A7_EKRN230034969-1A_HHG75DSX7_L2_2.fq.gz A7_EKRN230034969-1A_HHG75DSX7_L2_1.fq.gz fastq fastq 8875539300.0 29585131.0 A7 EKRN230034969 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:2426453238;C:2049446891;G:2017593291;T:2382011570;N:34310 150 150     2426453238 2049446891 2017593291 2382011570 34310 SRX22482171 SRS19495552 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.92101 0.92052 0.12337 0.12369 0.74052 0.74012 0.47692 0.47624 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28886 28886 SRR26783951 SRX22482170 SRS19495551 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         ETV6::RUNX1 tumor #6   isolate:ETV6::RUNX1 knock in zebrafish #6|age:9 month 16 month|collection date:2023 03 08|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: leukemic whole kidney marrow #6 A6 A6 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A6_EKRN230034968-1A_HHG75DSX7_L2_1.fq.gz A6_EKRN230034968-1A_HHG75DSX7_L2_2.fq.gz fastq fastq 7560052500.0 25200175.0 A6 EKRN230034968 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:2044845958;C:1762698184;G:1744547769;T:2007930943;N:29646 150 150     2044845958 1762698184 1744547769 2007930943 29646 SRX22482170 SRS19495551 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.92673 0.92704 0.11586 0.1157 0.73464 0.73454 0.49457 0.49107 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28887 28887 SRR26783952 SRX22482169 SRS19495550 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         ETV6::RUNX1 tumor #5   isolate:ETV6::RUNX1 knock in zebrafish #5|age:9 month 16 month|collection date:2023 03 07|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: leukemic whole kidney marrow #5 A5 A5 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A5_EKRN230034967-1A_HHG75DSX7_L2_1.fq.gz A5_EKRN230034967-1A_HHG75DSX7_L2_2.fq.gz fastq fastq 8269320000.0 27564400.0 A5 EKRN230034967 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:2208684304;C:1954270073;G:1933348989;T:2172985012;N:31622 150 150     2208684304 1954270073 1933348989 2172985012 31622 SRX22482169 SRS19495550 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.94285 0.9422 0.08987 0.08977 0.75507 0.7541 0.52032 0.50956 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28888 28888 SRR26783953 SRX22482168 SRS19495549 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         ETV6::RUNX1 tumor #4   isolate:ETV6::RUNX1 knock in zebrafish #4|age:9 month 16 month|collection date:2023 02 06|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: leukemic whole kidney marrow #4 A4 A4 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A4_EKRN230034966-1A_HHG75DSX7_L2_2.fq.gz A4_EKRN230034966-1A_HHG75DSX7_L2_1.fq.gz fastq fastq 6514998000.0 21716660.0 A4 EKRN230034966 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:1755226695;C:1525196740;G:1509297214;T:1725251790;N:25561 150 150     1755226695 1525196740 1509297214 1725251790 25561 SRX22482168 SRS19495549 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.93241 0.93171 0.08147 0.08039 0.72318 0.72271 0.48554 0.48715 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28889 28889 SRR26783954 SRX22482167 SRS19495548 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         ETV6::RUNX1 tumor #3   isolate:ETV6::RUNX1 knock in zebrafish #3|age:9 month 16 month|collection date:2023 02 05|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: leukemic whole kidney marrow #3 A3 A3 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A3_EKRN230034965-1A_HHG75DSX7_L2_1.fq.gz A3_EKRN230034965-1A_HHG75DSX7_L2_2.fq.gz fastq fastq 7439426700.0 24798089.0 A3 EKRN230034965 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:1997063524;C:1750471227;G:1730255985;T:1961607399;N:28565 150 150     1997063524 1750471227 1730255985 1961607399 28565 SRX22482167 SRS19495548 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.93247 0.93234 0.10911 0.10805 0.73359 0.73377 0.49804 0.4981 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28890 28890 SRR26783955 SRX22482166 SRS19495547 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         Non leukemic kidney marrow control #3   isolate:UAS::GFP control #3|age:9 month 16 month|collection date:2023 01 13|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: non leukemic whole kidney marrow #3 A11 A11 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A11_EKRN230034973-1A_HHG75DSX7_L2_1.fq.gz A11_EKRN230034973-1A_HHG75DSX7_L2_2.fq.gz fastq fastq 7535572200.0 25118574.0 A11 EKRN230034973 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:2030032446;C:1757927547;G:1745325371;T:2002258226;N:28610 150 150     2030032446 1757927547 1745325371 2002258226 28610 SRX22482166 SRS19495547 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.93698 0.93781 0.07017 0.0697 0.72324 0.72316 0.52767 0.52695 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28891 28891 SRR26783956 SRX22482165 SRS19495546 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         ETV6::RUNX1 tumor #2   isolate:ETV6::RUNX1 knock in zebrafish #2|age:9 month 16 month|collection date:2023 01 04|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: leukemic whole kidney marrow #2 A2 A2 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A2_EKRN230034964-1A_HHG75DSX7_L2_1.fq.gz A2_EKRN230034964-1A_HHG75DSX7_L2_2.fq.gz fastq fastq 8139110700.0 27130369.0 A2 EKRN230034964 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:2200986080;C:1900110630;G:1876627982;T:2161354090;N:31918 150 150     2200986080 1900110630 1876627982 2161354090 31918 SRX22482165 SRS19495546 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.93418 0.93374 0.11817 0.11792 0.73227 0.73251 0.49375 0.49338 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system
28892 28892 SRR26783957 SRX22482164 SRS19495545 SRP471222 PRJNA1038711 Zebrafish leukemia sequencing PRJNA1038711 Other Validation of an ETV6::RUNX1 positive pB ALL zebrafish model         ETV6::RUNX1 tumor #1   isolate:ETV6::RUNX1 knock in zebrafish #1|age:9 month 16 month|collection date:2023 01 03|geo loc name:Finland: Tampere Europe|sex:female|tissue:Kidney marrow|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: leukemic whole kidney marrow #1 A1 A1 PCR     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq X   SRP471222     A1_EKRN230034963-1A_HHG75DSX7_L2_1.fq.gz A1_EKRN230034963-1A_HHG75DSX7_L2_2.fq.gz fastq fastq 10375495200.0 34584984.0 A1 EKRN230034963 1A HHG75DSX7 L2 1.fq.gz 0:150 1:150 A:2781268558;C:2442675432;G:2417292722;T:2734218470;N:40018 150 150     2781268558 2442675432 2417292722 2734218470 40018 SRX22482164 SRS19495545 SRA1748743 Tampere University|Clinical Medicine Tampere University 2 0.93836 0.93801 0.12376 0.12224 0.74416 0.74406 0.49065 0.48915 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Finland 2023-11-10 Adult Adult Multi-tissue Multi-system

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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");;