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20 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "PCR" and technology = "bulk"

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tissue_curation_coarse 2

tissue_curation 2

devstage_curation_coarse 2

devstage_curation 2

technology 1

  • bulk · 20 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PCR · 20 ✖

experiment.library_layout 1

  • PAIRED · 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
32476 32476 SRR29270149 SRX24787634 SRS21505104 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Mut 20 1   strain:AB|age:20|collection date:2023 06 10|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Mut 20 1 E10 E10 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Mut-20-1_S162_R1.fastq.gz foxl2l_Mut-20-1_S162_R2.fastq.gz fastq fastq 8940963680.0 29605840.0 foxl2l Mut 20 1 S162 R1.fastq.gz 0:151 1:151 A:2232167098;C:2229744850;G:2271326718;T:2207692629;N:32385 151 151     2232167098 2229744850 2271326718 2207692629 32385 SRX24787634 SRS21505104 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32477 32477 SRR29270150 SRX24787633 SRS21505103 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Het 20 3   strain:AB|age:20|collection date:2023 06 09|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Het 20 3 E9 E9 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Het-20-3_S161_R1.fastq.gz foxl2l_Het-20-3_S161_R2.fastq.gz fastq fastq 7038409282.0 23305991.0 foxl2l Het 20 3 S161 R1.fastq.gz 0:151 1:151 A:1766863186;C:1740008639;G:1787471686;T:1744039429;N:26342 151 151     1766863186 1740008639 1787471686 1744039429 26342 SRX24787633 SRS21505103 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32478 32478 SRR29270151 SRX24787632 SRS21505102 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Het 20 2   strain:AB|age:20|collection date:2023 06 08|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Het 20 2 E8 E8 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Het-20-2_S160_R1.fastq.gz foxl2l_Het-20-2_S160_R2.fastq.gz fastq fastq 6772505832.0 22425516.0 foxl2l Het 20 2 S160 R1.fastq.gz 0:151 1:151 A:1704124986;C:1673138074;G:1713003931;T:1682214009;N:24832 151 151     1704124986 1673138074 1713003931 1682214009 24832 SRX24787632 SRS21505102 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32479 32479 SRR29270152 SRX24787631 SRS21505101 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Het 20 1   strain:AB|age:20|collection date:2023 06 07|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Het 20 1 E7 E7 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Het-20-1_S159_R1.fastq.gz foxl2l_Het-20-1_S159_R2.fastq.gz fastq fastq 11685740812.0 38694506.0 foxl2l Het 20 1 S159 R1.fastq.gz 0:151 1:151 A:2939618668;C:2888861085;G:2958173208;T:2899044704;N:43147 151 151     2939618668 2888861085 2958173208 2899044704 43147 SRX24787631 SRS21505101 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32480 32480 SRR29270153 SRX24787630 SRS21505100 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Mut 15 3   strain:AB|age:15|collection date:2023 06 06|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Mut 15 3 E6 E6 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Mut-15-3_S158_R1.fastq.gz foxl2l_Mut-15-3_S158_R2.fastq.gz fastq fastq 9503789604.0 31469502.0 foxl2l Mut 15 3 S158 R1.fastq.gz 0:151 1:151 A:2393052443;C:2340958111;G:2411502428;T:2358240313;N:36309 151 151     2393052443 2340958111 2411502428 2358240313 36309 SRX24787630 SRS21505100 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32481 32481 SRR29270154 SRX24787629 SRS21505099 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Mut 15 2   strain:AB|age:15|collection date:2023 06 05|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Mut 15 2 E5 E5 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Mut-15-2_S157_R1.fastq.gz foxl2l_Mut-15-2_S157_R2.fastq.gz fastq fastq 7416837026.0 24559063.0 foxl2l Mut 15 2 S157 R1.fastq.gz 0:151 1:151 A:1865711045;C:1830489703;G:1881612508;T:1838995980;N:27790 151 151     1865711045 1830489703 1881612508 1838995980 27790 SRX24787629 SRS21505099 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32482 32482 SRR29270155 SRX24787628 SRS21505098 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Mut 15 1   strain:AB|age:15|collection date:2023 06 04|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Mut 15 1 E4 E4 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Mut-15-1_S156_R1.fastq.gz foxl2l_Mut-15-1_S156_R2.fastq.gz fastq fastq 7092721868.0 23485834.0 foxl2l Mut 15 1 S156 R1.fastq.gz 0:151 1:151 A:1764166761;C:1770534219;G:1820397492;T:1737597123;N:26273 151 151     1764166761 1770534219 1820397492 1737597123 26273 SRX24787628 SRS21505098 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32483 32483 SRR29270156 SRX24787627 SRS21505097 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Het 15 3   strain:AB|age:15|collection date:2023 06 03|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Het 15 3 E3 E3 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Het-15-3_S155_R1.fastq.gz foxl2l_Het-15-3_S155_R2.fastq.gz fastq fastq 8083606820.0 26766910.0 foxl2l Het 15 3 S155 R1.fastq.gz 0:151 1:151 A:2028557443;C:2001113164;G:2050610840;T:2003295953;N:29420 151 151     2028557443 2001113164 2050610840 2003295953 29420 SRX24787627 SRS21505097 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32484 32484 SRR29270157 SRX24787626 SRS21505096 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Mut 20 3   strain:AB|age:20|collection date:2023 06 12|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Mut 20 3 E12 E12 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Mut-20-3_S164_R1.fastq.gz foxl2l_Mut-20-3_S164_R2.fastq.gz fastq fastq 7474861796.0 24751198.0 foxl2l Mut 20 3 S164 R1.fastq.gz 0:151 1:151 A:1878881650;C:1849512621;G:1891142525;T:1855296720;N:28280 151 151     1878881650 1849512621 1891142525 1855296720 28280 SRX24787626 SRS21505096 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32485 32485 SRR29270158 SRX24787625 SRS21505095 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Mut 20 2   strain:AB|age:20|collection date:2023 06 11|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Mut 20 2 E11 E11 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Mut-20-2_S163_R1.fastq.gz foxl2l_Mut-20-2_S163_R2.fastq.gz fastq fastq 8203704066.0 27164583.0 foxl2l Mut 20 2 S163 R1.fastq.gz 0:151 1:151 A:2061693689;C:2030126562;G:2072980952;T:2038873198;N:29665 151 151     2061693689 2030126562 2072980952 2038873198 29665 SRX24787625 SRS21505095 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32486 32486 SRR29270159 SRX24787624 SRS21505094 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Het 15 2   strain:AB|age:15|collection date:2023 06 02|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Het 15 2 E2 E2 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Het-15-2_S154_R1.fastq.gz foxl2l_Het-15-2_S154_R2.fastq.gz fastq fastq 7868286860.0 26053930.0 foxl2l Het 15 2 S154 R1.fastq.gz 0:151 1:151 A:1972210357;C:1946891859;G:2008091153;T:1941064817;N:28674 151 151     1972210357 1946891859 2008091153 1941064817 28674 SRX24787624 SRS21505094 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
32487 32487 SRR29270160 SRX24787623 SRS21505093 SRP511487 PRJNA1119569 RNA seq of zebrafish foxl2l mutant PRJNA1119569 Other Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.         foxl2l Het 15 1   strain:AB|age:15|collection date:2023 06 01|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal                 foxl2l Het 15 1 E1 E1 50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   SRP511487     foxl2l_Het-15-1_S153_R1.fastq.gz foxl2l_Het-15-1_S153_R2.fastq.gz fastq fastq 7117391946.0 23567523.0 foxl2l Het 15 1 S153 R1.fastq.gz 0:151 1:151 A:1795668098;C:1752824783;G:1793720116;T:1775153584;N:25365 151 151     1795668098 1752824783 1793720116 1775153584 25365 SRX24787623 SRS21505093 SRA1887976 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk bulk bulk   China 2024-06-03 Undetermined Undetermined Gonad Reproductive System
70803 70803 SRR20651070 SRX16674147 SRS14305696 SRP388214 PRJNA861969 RNA seq in KLHL40 KO zebrafish muscle PRJNA861969 Other Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.       klhl40a KO4 klhl40a Mutant 4   strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal                 KO4 klhl40a4 klhl40a4 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP388214     KO4_1.fq.gz KO4_2.fq.gz fastq fastq 6711352800.0 22371176.0 KO4 1.fq.gz 0:150 1:150 A:1777166363;C:1589553466;G:1610514347;T:1734012530;N:106094 150 150     1777166363 1589553466 1610514347 1734012530 106094 SRX16674147 SRS14305696     Brigham and Women's Hospital 2 0.96541 0.96534 0.04564 0.04561 0.80478 0.80594 0.49645 0.49712 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk bulk bulk   United States 2022-07-26 Adult Adult Muscle Muscular System
70804 70804 SRR20651071 SRX16674146 SRS14305695 SRP388214 PRJNA861969 RNA seq in KLHL40 KO zebrafish muscle PRJNA861969 Other Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.       klhl40a KO3 klhl40a Mutant 3   strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal                 KO3 klhl40a3 klhl40a3 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP388214     KO3_1.fq.gz KO3_2.fq.gz fastq fastq 6837271200.0 22790904.0 KO3 1.fq.gz 0:150 1:150 A:1889665334;C:1538962427;G:1555674788;T:1852860913;N:107738 150 150     1889665334 1538962427 1555674788 1852860913 107738 SRX16674146 SRS14305695     Brigham and Women's Hospital 2 0.9394 0.93825 0.07858 0.07822 0.7413 0.74186 0.50534 0.49292 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk bulk bulk   United States 2022-07-26 Adult Adult Muscle Muscular System
70805 70805 SRR20651072 SRX16674145 SRS14305694 SRP388214 PRJNA861969 RNA seq in KLHL40 KO zebrafish muscle PRJNA861969 Other Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.       klhl40a KO2 klhl40a Mutant 2   strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal                 KO2 klhl40a2 klhl40a2 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP388214     KO2_1.fq.gz KO2_2.fq.gz fastq fastq 6551044800.0 21836816.0 KO2 1.fq.gz 0:150 1:150 A:1793351007;C:1490899611;G:1511714794;T:1754976004;N:103384 150 150     1793351007 1490899611 1511714794 1754976004 103384 SRX16674145 SRS14305694     Brigham and Women's Hospital 2 0.95416 0.953 0.06534 0.06511 0.76678 0.76668 0.51901 0.49628 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk bulk bulk   United States 2022-07-26 Adult Adult Muscle Muscular System
70806 70806 SRR20651073 SRX16674144 SRS14305693 SRP388214 PRJNA861969 RNA seq in KLHL40 KO zebrafish muscle PRJNA861969 Other Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.       klh40a KO1 klhl40a Mutant 1   strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal                 KO1 klhl40a1 klhl40a1 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP388214     KO1_1.fq.gz KO1_2.fq.gz fastq fastq 7080009000.0 23600030.0 KO1 1.fq.gz 0:150 1:150 A:1927450674;C:1619718617;G:1639235237;T:1893497462;N:107010 150 150     1927450674 1619718617 1639235237 1893497462 107010 SRX16674144 SRS14305693     Brigham and Women's Hospital 2 0.94175 0.94193 0.06579 0.06628 0.75045 0.7503 0.49508 0.50075 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk bulk bulk   United States 2022-07-26 Adult Adult Muscle Muscular System
70807 70807 SRR20651074 SRX16674143 SRS14305692 SRP388214 PRJNA861969 RNA seq in KLHL40 KO zebrafish muscle PRJNA861969 Other Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.       WT4 Wild type Control4   strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal                 WT4 WT4 WT4 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP388214     WT4_1.fq.gz WT4_2.fq.gz fastq fastq 7079022600.0 23596742.0 WT4 1.fq.gz 0:150 1:150 A:1901387601;C:1651068590;G:1657216811;T:1869243020;N:106578 150 150     1901387601 1651068590 1657216811 1869243020 106578 SRX16674143 SRS14305692     Brigham and Women's Hospital 2 0.95455 0.95486 0.07809 0.07798 0.75491 0.75442 0.49622 0.50833 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk bulk bulk   United States 2022-07-26 Adult Adult Muscle Muscular System
70808 70808 SRR20651075 SRX16674142 SRS14305691 SRP388214 PRJNA861969 RNA seq in KLHL40 KO zebrafish muscle PRJNA861969 Other Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.       WT3 Wild type Control3   strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal                 WT3 WT3 WT3 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP388214     WT3_1.fq.gz WT3_2.fq.gz fastq fastq 6750141600.0 22500472.0 WT3 1.fq.gz 0:150 1:150 A:1809694888;C:1570721302;G:1597114393;T:1772508410;N:102607 150 150     1809694888 1570721302 1597114393 1772508410 102607 SRX16674142 SRS14305691     Brigham and Women's Hospital 2 0.95657 0.95647 0.06172 0.06163 0.76252 0.76366 0.49411 0.49204 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk bulk bulk   United States 2022-07-26 Adult Adult Muscle Muscular System
70809 70809 SRR20651076 SRX16674141 SRS14305690 SRP388214 PRJNA861969 RNA seq in KLHL40 KO zebrafish muscle PRJNA861969 Other Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.       WT2 Wild type Control2   strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal                 WT2 WT2 WT2 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP388214     WT2_1.fq.gz WT2_2.fq.gz fastq fastq 6786893400.0 22622978.0 WT2 1.fq.gz 0:150 1:150 A:1835782156;C:1564402670;G:1586345899;T:1800260025;N:102650 150 150     1835782156 1564402670 1586345899 1800260025 102650 SRX16674141 SRS14305690     Brigham and Women's Hospital 2 0.95057 0.9495 0.06714 0.06726 0.75266 0.75333 0.50647 0.50457 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk bulk bulk   United States 2022-07-26 Adult Adult Muscle Muscular System
70810 70810 SRR20651077 SRX16674140 SRS14305689 SRP388214 PRJNA861969 RNA seq in KLHL40 KO zebrafish muscle PRJNA861969 Other Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.       WT1 Wild type Control1   strain:AB|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 Months|dev stage:Adult|sex:male|tissue:Skeletal Muscle|disease:Nemaline Myopathy|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal                 WT1 WT1 WT1 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP388214     WT1_1.fq.gz WT1_2.fq.gz fastq fastq 6946359900.0 23154533.0 WT1 1.fq.gz 0:150 1:150 A:1891340276;C:1588097676;G:1606011156;T:1860805584;N:105208 150 150     1891340276 1588097676 1606011156 1860805584 105208 SRX16674140 SRS14305689     Brigham and Women's Hospital 2 0.94444 0.94509 0.07758 0.07756 0.72943 0.72878 0.50732 0.50723 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk bulk bulk   United States 2022-07-26 Adult Adult Muscle Muscular 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");;