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20 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RT-PCR" and tissue_curation = "Embryo Imprecise"

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devstage_curation_coarse 3

devstage_curation 3

experiment.library_strategy 2

tissue_curation_coarse 1

tissue_curation 1

  • Embryo Imprecise · 20 ✖

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 20 ✖

experiment.library_layout 1

  • SINGLE · 20 ✖
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
30599 30599 SRR27865238 SRX23527802 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con MO 6 6 con MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     con-KDM_1.fq.gz con-KDM_2.fq.gz fastq fastq 7088132100.0 23627107.0 con KDM 1.fq.gz 0:150 1:150 A:1893419600;C:1649526065;G:1662549202;T:1882459200;N:178033 150 150     1893419600 1649526065 1662549202 1882459200 178033 SRX23527802 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30600 30600 SRR27865239 SRX23527801 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 KDM4C MO 5 5 KDM4C MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     KDM-MO_1.fq.gz KDM-MO_2.fq.gz fastq fastq 7876840500.0 26256135.0 KDM MO 1.fq.gz 0:150 1:150 A:2104173142;C:1831662159;G:1843980192;T:2096831538;N:193469 150 150     2104173142 1831662159 1843980192 2096831538 193469 SRX23527801 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30601 30601 SRR27865240 SRX23527800 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 ZNF662 MO 4 4 ZNF662 MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     znf547-MO_1.fq.gz znf547-MO_2.fq.gz fastq fastq 7573815300.0 25246051.0 znf547 MO 1.fq.gz 0:150 1:150 A:2014197761;C:1766587259;G:1782217029;T:2010540623;N:272628 150 150     2014197761 1766587259 1782217029 2010540623 272628 SRX23527800 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30602 30602 SRR27865241 SRX23527799 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 SEMA5A RNA 3 3 SEMA5A RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     semRNA_1.fq.gz semRNA_2.fq.gz fastq fastq 5575566000.0 18585220.0 semRNA 1.fq.gz 0:150 1:150 A:1456001758;C:1325628099;G:1339796989;T:1454076989;N:62165 150 150     1456001758 1325628099 1339796989 1454076989 62165 SRX23527799 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30603 30603 SRR27865242 SRX23527798 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 MT ATP6 RNA 2 2 MT ATP6 RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     ATP6-RNA_1.fq.gz ATP6-RNA_2.fq.gz fastq fastq 5437771200.0 18125904.0 ATP6 RNA 1.fq.gz 0:150 1:150 A:1438540045;C:1272310670;G:1290121053;T:1436739799;N:59633 150 150     1438540045 1272310670 1290121053 1436739799 59633 SRX23527798 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30604 30604 SRR27865243 SRX23527797 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con RNA 1 1 con RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     con-RNA_1.fq.gz con-RNA_2.fq.gz fastq fastq 6733158900.0 22443863.0 con RNA 1.fq.gz 0:150 1:150 A:1766014369;C:1595337569;G:1610127771;T:1761604971;N:74220 150 150     1766014369 1595337569 1610127771 1761604971 74220 SRX23527797 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
33326 33326 SRR29962931 SRX25444536 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 zx150 RNAseq 4 4 zx150 RNAseq     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     zx150_input_1.fq.gz zx150_input_2.fq.gz fastq fastq 11540682300.0 38468941.0 zx150 input 1.fq.gz 0:150 1:150 A:3038586049;C:2720235923;G:2771004747;T:3010645578;N:210003 150 150     3038586049 2720235923 2771004747 3010645578 210003 SRX25444536 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33327 33327 SRR29962932 SRX25444535 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con RNAseq 3 3 con RNAseq     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     con-zx150_input_1.fq.gz con-zx150_input_2.fq.gz fastq fastq 11610174300.0 38700581.0 con zx150 input 1.fq.gz 0:150 1:150 A:3049654977;C:2746004045;G:2795023766;T:3019280685;N:210827 150 150     3049654977 2746004045 2795023766 3019280685 210827 SRX25444535 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33328 33328 SRR29962933 SRX25444534 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 zx150 m6A 2 2 zx150 m6A     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     zx150_IP_1.fq.gz zx150_IP_2.fq.gz fastq fastq 17410816801.0 80469610.0 zx150 IP 1.fq.gz 0:108.79 1:107.58 A:4434870667;C:3759430468;G:4812205613;T:4404166470;N:143583 108 107     4434870667 3759430468 4812205613 4404166470 143583 SRX25444534 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33329 33329 SRR29962934 SRX25444533 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con m6A 1 1 con m6A     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     con-zx150_IP_1.fq.gz con-zx150_IP_2.fq.gz fastq fastq 16822889423.0 77865752.0 con zx150 IP 1.fq.gz 0:108.68 1:107.37 A:4324048234;C:3668630618;G:4601614069;T:4228151501;N:445001 108 107     4324048234 3668630618 4601614069 4228151501 445001 SRX25444533 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
36663 36663 SRR800049 SRX257156 SRS405710 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq 5azaCyD control   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq 5azaCyD control sphere RNAseq 5azaCyD control 9323X2 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_5azaCyD_control_SE_9323X2_120628_SN141_0513_AD12CFACXX_4.txt.gz Illumina native 2563410950.0 51268219.0 9323X2 120628 SN141 0513 AD12CFACXX 4 0:50 A:663337120;C:603101927;G:752336300;T:542924123;N:1711480 50       663337120 603101927 752336300 542924123 1711480 SRX257156 SRS405710 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.65713   0.09976   0.81677   0.81063   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-05-07 Blastula Embryo Embryo Imprecise All anatomical structures
36664 36664 SRR800046 SRX257155 SRS405709 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq 5azaCyD treatment   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq 5azaCyD treatment sphere RNAseq 5azaCyD treatment 9323X1 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_5azaCyD_treatment_SE_9323X1_120628_SN141_0513_AD12CFACXX_4.txt.gz Illumina native 2595654550.0 51913091.0 9323X1 120628 SN141 0513 AD12CFACXX 4 0:50 A:676999669;C:618386951;G:759497082;T:539035799;N:1735049 50       676999669 618386951 759497082 539035799 1735049 SRX257155 SRS405709 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.76926   0.12287   0.82408   0.72244   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-04-03 Blastula Embryo Embryo Imprecise All anatomical structures
71388 71388 SRR21528734 SRX17531094 SRS15079603 SRP396673 PRJNA879284 Toxicology evaluation of overdose hydroxychloroquine on zebrafish Danio rerio embryos PRJNA879284 Other         HCQ embryos HCQ embryos   strain:AB|breed:Egg water|age:0.8year|dev stage:5hpf|sex:not applicable|tissue:embryo|cell line:embryo|cell type:embryo|collected by:Straw|BioSampleModel:Model organism or animal                 RNA Seq of HCQ embryo 2 2 HCQ embryo     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP396673     HCQ_1.fq.gz HCQ_2.fq.gz fastq fastq 6247416600.0 20824722.0 HCQ 1.fq.gz 0:150 1:150 A:1705532494;C:1419469418;G:1445959454;T:1676101471;N:353763 150 150     1705532494 1419469418 1445959454 1676101471 353763 SRX17531094 SRS15079603 SRA1495070 Sichuan University|West China Second University Hospital Sichuan University 2 0.95531 0.95352 0.05755 0.05707 0.7513 0.75215 0.48749 0.48711 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-09-12 Multi-stage Multi-stage Embryo Imprecise All anatomical structures
71389 71389 SRR21528735 SRX17531093 SRS15079603 SRP396673 PRJNA879284 Toxicology evaluation of overdose hydroxychloroquine on zebrafish Danio rerio embryos PRJNA879284 Other         HCQ embryos HCQ embryos   strain:AB|breed:Egg water|age:0.8year|dev stage:5hpf|sex:not applicable|tissue:embryo|cell line:embryo|cell type:embryo|collected by:Straw|BioSampleModel:Model organism or animal                 RNA Seq of WT embryo 1 1 WT embryo     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP396673     HCQ-con_1.fq.gz HCQ-con_2.fq.gz fastq fastq 6039833100.0 20132777.0 HCQ con 1.fq.gz 0:150 1:150 A:1632793916;C:1383182551;G:1413411225;T:1610087974;N:357434 150 150     1632793916 1383182551 1413411225 1610087974 357434 SRX17531093 SRS15079603 SRA1495070 Sichuan University|West China Second University Hospital Sichuan University 2 0.95216 0.95061 0.05402 0.05357 0.75185 0.75262 0.48712 0.48749 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-09-12 Multi-stage Multi-stage Embryo Imprecise All anatomical structures
75644 75644 SRR24752590 SRX20528694 SRS17837826 SRP439887 PRJNA976915 Embryotoxicity evaluation of Gentamicin using the zebrafish model PRJNA976915 Other Embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model       Embryos 5hpf Embryos 5hpf   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal                 RNA Seq of Embryo 5hpf Gentanicin 2 2 Embryo 5hpf Gentanicin     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP439887     Qingda_1.fq.gz Qingda_2.fq.gz fastq fastq 6985244400.0 23284148.0 Qingda 1.fq.gz 0:150 1:150 A:1634658220;C:1842974934;G:1881072995;T:1626517291;N:20960 150 150     1634658220 1842974934 1881072995 1626517291 20960 SRX20528694 SRS17837826 SRA1645398 Sichuan University|West China Second University Hospital Sichuan University 2 0.96818 0.97235 0.21368 0.21914 0.79265 0.79273 0.53525 0.50366 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2023-05-27 Blastula Embryo Embryo Imprecise All anatomical structures
75645 75645 SRR24752591 SRX20528693 SRS17837826 SRP439887 PRJNA976915 Embryotoxicity evaluation of Gentamicin using the zebrafish model PRJNA976915 Other Embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model       Embryos 5hpf Embryos 5hpf   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal                 RNA Seq of WT Embryo 5hpf 1 1 WT Embryo 5hpf     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP439887     WT-blank_1.fq.gz WT-blank_2.fq.gz fastq fastq 6062337300.0 20207791.0 WT blank 1.fq.gz 0:150 1:150 A:1526499059;C:1498285888;G:1526586728;T:1510947161;N:18464 150 150     1526499059 1498285888 1526586728 1510947161 18464 SRX20528693 SRS17837826 SRA1645398 Sichuan University|West China Second University Hospital Sichuan University 2 0.96896 0.97182 0.02595 0.02539 0.77861 0.77865 0.48078 0.48377 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2023-05-27 Blastula Embryo Embryo Imprecise All anatomical structures
75646 75646 SRR24754508 SRX20530612 SRS17839502 SRP439912 PRJNA976946 MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model PRJNA976946 Other MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model       m6A Embryos 5hpf m6A Embryos 5hpf   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal                 MeRIP Seq of Embryo 5hpf Gentanicin 2 2 Embryo 5hpf Gentanicin     RIP-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP439912     QingdaIP_1.fq.gz QingdaIP_2.fq.gz Qingdainput_1.fq.gz Qingdainput_2.fq.gz fastq fastq fastq fastq 16015155900.0 53383853.0 QingdaIP 1.fq.gz 0:150 1:150 A:3341079522;C:3427050846;G:6045646273;T:3201293287;N:85972 150 150     3341079522 3427050846 6045646273 3201293287 85972 SRX20530612 SRS17839502 SRA1645459 Sichuan University|West China Second University Hospital Sichuan University 2 0.75159 0.73659 0.1359 0.13542 0.8117 0.81172 0.51543 0.51251 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2023-05-27 Blastula Embryo Embryo Imprecise All anatomical structures
75647 75647 SRR24754509 SRX20530611 SRS17839502 SRP439912 PRJNA976946 MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model PRJNA976946 Other MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model       m6A Embryos 5hpf m6A Embryos 5hpf   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal                 MeRIP Seq of WT Embryo 5hpf 1 1 WT Embryo 5hpf     RIP-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP439912     WT-blankIP_1.fq.gz WT-blankIP_2.fq.gz WT-blankinput_1.fq.gz WT-blankinput_2.fq.gz fastq fastq fastq fastq 15326922600.0 51089742.0 WT blankIP 1.fq.gz 0:150 1:150 A:3289509867;C:3239692571;G:5510216977;T:3287142341;N:360844 150 150     3289509867 3239692571 5510216977 3287142341 360844 SRX20530611 SRS17839502 SRA1645459 Sichuan University|West China Second University Hospital Sichuan University 2 0.71182 0.69789 0.02169 0.02058 0.80409 0.80395 0.47813 0.48125 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2023-05-27 Blastula Embryo Embryo Imprecise All anatomical structures
77327 77327 SRR065197 SRX026483 SRS114570 SRP003472 PRJXX3472 RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation ZF_U1C Transcriptome Analysis Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation.   pubmed:21468032 Total RNA from 3 dpf mutant zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library. Total RNA from 3 dpf mutant zebrafish embryos MUT                     3 dpf mutant zebrafish embryos MUT mut 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> SRP003472     MUT_1.txt.tar.gz MUT_2N.txt.tar.gz MUT_3.txt.tar.gz fastq fastq fastq 2418427464.0 31821414.0 MUT 0:76 A:604956506;C:600954722;G:608767958;T:600808464;N:2939814 76       604956506 600954722 608767958 600808464 2939814 SRX026483 SRS114570     Justus-Liebig University Giessen 1 0.91109   0.077   0.71445   0.44387   76   B   usable mapping rate illumina early_illumina unknown other unknown bulk unknown unknown   Germany 2011-03-31 Larval Larval Embryo Imprecise All anatomical structures
77328 77328 SRR065196 SRX026482 SRS114569 SRP003472 PRJXX3472 RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation ZF_U1C Transcriptome Analysis Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation.   pubmed:21468032 Total RNA from 3 dpf wildtype zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library. Total RNA from 3 dpf wildtype zebrafish embryos WT                     3 dpf wildtype embryos WT wt 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> SRP003472     WT_1.txt.tar WT_2.txt.tar.gz WT_3.txt.tar.gz WT_4.txt.tar.gz fastq fastq fastq fastq 2697785376.0 35497176.0 WT 0:76 A:676186765;C:669131645;G:670872323;T:676745206;N:4849437 76       676186765 669131645 670872323 676745206 4849437 SRX026482 SRS114569     Justus-Liebig University Giessen 1 0.9435   0.087   0.71429   0.46075   76   B   usable mapping rate illumina early_illumina unknown other unknown bulk unknown unknown   Germany 2011-03-31 Larval Larval 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");;