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
38302,SRR1695730,SRX798420,SRS781712,SRP050879,PRJNA269540,zebrafish transciptsome sequencing,PRJNA269540,Other,we aimed to calculate the expression level of some special genes,,,,Testis from Danio rerio,testis of zebrafish,,strain:AB|dev stage:adult|sex:male|tissue:testis|biomaterial provider:zebrafish facilities of the Institute of Hydrobiology  Chinese Academy of Sciences|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish testis,testis of zebrafish,Zebrafish facilities of the Institute of Hydrobiology  Chinese Academy of Sciences,Wild type zebrafish from an AB background were maintained in the zebrafish facilities of the Institute of Hydrobiology  Chinese Academy of Sciences. Testis of adult is collected for RNA extraction. Total RNA extraction was performed with TRIZOL reagents from Takara following the manufacturer’s instructions. Total RNA contents were measured using the NanoDrop 2000. Then 5 μg total RNA was used for mRNA isolation with oligo dT magnetic beads and fragmented into small pieces in fragmentation buffer at 70°C for 4 min before cDNA synthesis. First strand cDNA was synthesized from the cleaved RNA using SuperScript II reverse transcriptase and random hexamer primers  followed by second strand cDNA synthesis using DNA polymerase I and RNaseH. post purification with a QIAquick PCR Purification Kit Qiagen  Dusseldorf  Germany  the double stranded cDNA was treated to repair ends by T4 DNA polymerase  Klenow enzyme  and T4 polynucleotide kinase NEB. This was followed by addition of a single A base using Klenow exo polymerase and ligation with an adapter using DNA ligase NEB. post ligation  the DNA was purified using a QIAquick PCR Purification Kit. PCR amplification with 10 to 12 cycles was performed with primers complementary to the adapter sequences to enrich the samples for the desired fragments. post purification using a QIAquick PCR Purification Kit  the product was dissolved in 30 µL of Qiagen EB buffer. These DNA fragments represented the designated mRNA library. The cDNA library was quantified with Qubit Invitrogen and a cluster of the DNA fragment was amplified using bridge PCR on the surface of a flow cell chip. Multiplexed libraries were sequenced for 101bp at both ends using an Illumina HiSeqTM 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP050879,,,Zebrafish_256-T14-VI_good_1.fq.gz Zebrafish_256-T14-VI_good_2.fq.gz,fastq fastq,5252571430.0,26005174.0,testis of zebrafish,0:100.99 1:100.99,A:1353125230;C:1273042497;G:1273793183;T:1350916239;N:1694281,100,100,,,1353125230,1273042497,1273793183,1350916239,1694281,SRX798420,SRS781712,SRA210676,CAS|systematic evolution,"Institute of Hydrobiology, Chinese Academy of sciences",2,0.93036,0.93332,0.09196,0.09372,0.64559,0.64806,0.48865,0.48746,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2015-09-23,Adult,Adult,Gonad,Reproductive System
41815,SRR5230754,SRX2539250,SRS1958964,SRP098895,PRJNA371444,transcriptome analyses of zebrafish preovulatory follicle cells,PRJNA371444,Other,To reveal downstream targets of progesterone receptor Pgr that are important for ovulation  RNA seq analyses were performed on isolated follicle cell samples from individual wild type and Pgr KO fish 3 each. The results revealed over 3000 genes and multiple pathways were significantly different between two genotypes  providing the first resource of genome wide data for investigating Pgr regulated ovulatory genes in basal vertebrate.,,pubmed:28111234,,,zebrafish follicle transcriptome,,strain:Tu|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:female|tissue:ovarian follicle cells|BioSampleModel:Model organism or animal,,,,,,,,,transcriptome of zebrafish preovulatory follicle cells from wt or Pgr knockout lines,C6RD4ANXX,C6RD4ANXX,To understand downstream targets of Pgr during ovulation  RNA SEQ were performed for preovulatory follicle cell samples from three wt and three pgrko fish respectively.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP098895,,,SL98515.fastq.gz SL98516.fastq.gz SL98517.fastq.gz SL98520.fastq.gz SL98519.fastq.gz SL98518.fastq.gz,fastq fastq fastq fastq fastq fastq,6949746750.0,138994935.0,SL98520.fastq.gz,0:50 1:0,A:1963366768;C:1504124031;G:1501663925;T:1979903691;N:688335,50,0,,,1963366768,1504124031,1501663925,1979903691,688335,SRX2539250,SRS1958964,SRA535744,East Carolina University|Biology,East Carolina University,1,0.88241,,0.58221,,0.71348,,0.48974,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-02-11,Adult,Adult,Gonad,Reproductive System
55230,SRR10199494,SRX6919650,SRS5450536,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTOV replicate 3,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:14 month|dev stage:sex mature|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  ovary,WT OV3,WT OV3,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-OV3_combined_R1.fastq.gz WT-OV3_combined_R2.fastq.gz,fastq fastq,7561018500.0,25203395.0,WT OV3 combined R1.fastq.gz,0:150 1:150,A:1960975544;C:1812551077;G:1817428088;T:1969970252;N:93539,150,150,,,1960975544,1812551077,1817428088,1969970252,93539,SRX6919650,SRS5450536,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.93185,0.9347,0.0198,0.0201,0.76114,0.76816,0.48035,0.48723,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Gonad,Reproductive System
55233,SRR10199497,SRX6919647,SRS5450533,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTOV replicate 1,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:12 month|dev stage:sex mature|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  ovary,WT OV1,WT OV1,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-OV1_combined_R1.fastq.gz WT-OV1_combined_R2.fastq.gz,fastq fastq,7084400700.0,23614669.0,WT OV1 combined R1.fastq.gz,0:150 1:150,A:1830047894;C:1703988911;G:1711436472;T:1838836910;N:90513,150,150,,,1830047894,1703988911,1711436472,1838836910,90513,SRX6919647,SRS5450533,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.93185,0.93459,0.02025,0.01982,0.76067,0.76589,0.48668,0.48174,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Gonad,Reproductive System
55234,SRR10199498,SRX6919646,SRS5450532,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23OV replicate 3,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:11 month|dev stage:sex mature|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  ovary,CHR23 OV3,CHR23 OV3,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-OV3_combined_R1.fastq.gz Chr23-OV3_combined_R2.fastq.gz,fastq fastq,6433822200.0,21446074.0,Chr23 OV3 combined R1.fastq.gz,0:150 1:150,A:1667018596;C:1543429194;G:1547966147;T:1675322985;N:85278,150,150,,,1667018596,1543429194,1547966147,1675322985,85278,SRX6919646,SRS5450532,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.93244,0.93333,0.02031,0.02045,0.76146,0.76575,0.48702,0.48221,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Gonad,Reproductive System
55235,SRR10199499,SRX6919645,SRS5450531,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23OV replicate 2,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:10 month|dev stage:sex mature|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  ovary,CHR23 OV2,CHR23 OV2,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-OV2_combined_R1.fastq.gz Chr23-OV2_combined_R2.fastq.gz,fastq fastq,6415269300.0,21384231.0,Chr23 OV2 combined R1.fastq.gz,0:150 1:150,A:1647742135;C:1552153098;G:1561042927;T:1654252320;N:78820,150,150,,,1647742135,1552153098,1561042927,1654252320,78820,SRX6919645,SRS5450531,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.93206,0.93587,0.01849,0.01908,0.7626,0.76873,0.48368,0.47779,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Gonad,Reproductive System
55236,SRR10199500,SRX6919644,SRS5450530,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23OV replicate 1,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:sex mature|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  ovary,CHR23 OV1,CHR23 OV1,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-OV1_combined_R1.fastq.gz Chr23-OV1_combined_R2.fastq.gz,fastq fastq,7023860100.0,23412867.0,Chr23 OV1 combined R1.fastq.gz,0:150 1:150,A:1812235215;C:1691491780;G:1699892771;T:1820155752;N:84582,150,150,,,1812235215,1691491780,1699892771,1820155752,84582,SRX6919644,SRS5450530,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.93341,0.93625,0.01967,0.01994,0.76264,0.76984,0.48352,0.48848,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Gonad,Reproductive System