RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

32 rows where experiment.library_selection = "PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Muscular System"

✎ View and edit SQL

This data as json, CSV (advanced)

technology 2

experiment.library_strategy 2

tissue_curation_coarse 1

  • Muscular System · 32 ✖

tissue_curation 1

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 32 ✖

experiment.library_selection 1

  • PCR · 32 ✖

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

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
29641 29641 SRR27397714 SRX23073965 SRS20033317 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library10 PG2   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 10|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS10 RRBS10 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG2_L7_1.fq.gz PG2_L7_2.fq.gz fastq fastq 981695400.0 3272318.0 PG2 L7 1.fq.gz 0:150 1:150 A:253124715;C:152724975;G:341105704;T:234698202;N:41804 150 150     253124715 152724975 341105704 234698202 41804 SRX23073965 SRS20033317 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0164 0.00047 0.01505 0.00036 0.9961 0.99965 0.58102 0.47058 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29642 29642 SRR27397715 SRX23073964 SRS20033316 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library9 PG1   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 9|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS9 RRBS9 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG1_L7_1.fq.gz PG1_L7_2.fq.gz fastq fastq 1157067600.0 3856892.0 PG1 L7 1.fq.gz 0:150 1:150 A:278308283;C:162228777;G:432676687;T:283803806;N:50047 150 150     278308283 162228777 432676687 283803806 50047 SRX23073964 SRS20033316 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02347 0.02319 0.02188 0.02162 0.99517 0.99519 0.50342 0.51027 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29643 29643 SRR27397716 SRX23073963 SRS20033315 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library8 LG4   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 8|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS8 RRBS8 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG4_L7_1.fq.gz LG4_L7_2.fq.gz fastq fastq 1080684300.0 3602281.0 LG4 L7 1.fq.gz 0:150 1:150 A:270759422;C:159278390;G:387693215;T:262907381;N:45892 150 150     270759422 159278390 387693215 262907381 45892 SRX23073963 SRS20033315 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01698 0.00033 0.01593 0.00026 0.99675 0.99979 0.4974 0.2 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29644 29644 SRR27397717 SRX23073962 SRS20033314 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library7 LG3   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 7|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS7 RRBS7 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG3_L7_1.fq.gz LG3_L7_2.fq.gz fastq fastq 1223063700.0 4076879.0 LG3 L7 1.fq.gz 0:150 1:150 A:301167012;C:182106743;G:443329321;T:296409064;N:51560 150 150     301167012 182106743 443329321 296409064 51560 SRX23073962 SRS20033314 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01787 0.01759 0.01644 0.01622 0.99545 0.99582 0.56826 0.56126 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29645 29645 SRR27397718 SRX23073961 SRS20033313 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library6 LG2   strain:ab|age:adult|collection date:2023 02 07|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 6|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS6 RRBS6 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG2_L7_1.fq.gz LG2_L7_2.fq.gz fastq fastq 1188600300.0 3962001.0 LG2 L7 1.fq.gz 0:150 1:150 A:294477343;C:172669379;G:418732939;T:302669966;N:50673 150 150     294477343 172669379 418732939 302669966 50673 SRX23073961 SRS20033313 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0205 0.02042 0.01903 0.01894 0.99584 0.99577 0.51685 0.51824 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29646 29646 SRR27397719 SRX23073960 SRS20033312 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library5 LG1   strain:ab|age:adult|collection date:2023 02 06|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 5|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS5 RRBS5 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG1_L7_1.fq.gz LG1_L7_2.fq.gz fastq fastq 1048183200.0 3493944.0 LG1 L7 1.fq.gz 0:150 1:150 A:260330612;C:163890192;G:372783427;T:251133569;N:45400 150 150     260330612 163890192 372783427 251133569 45400 SRX23073960 SRS20033312 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01999 0.00059 0.01851 0.00045 0.99563 0.99961 0.49816 0.36842 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29647 29647 SRR27397720 SRX23073959 SRS20033311 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library4 CG4   strain:ab|age:adult|collection date:2023 02 05|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 4|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS4 RRBS4 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG4_L7_1.fq.gz CG4_L7_2.fq.gz fastq fastq 1547200200.0 5157334.0 CG4 L7 1.fq.gz 0:150 1:150 A:389261224;C:230650937;G:559928386;T:367293552;N:66101 150 150     389261224 230650937 559928386 367293552 66101 SRX23073959 SRS20033311 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01121 0.00022 0.01024 0.00018 0.99713 0.99991 0.56111 1.0 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29648 29648 SRR27397721 SRX23073958 SRS20033310 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library3 CG3   strain:ab|age:adult|collection date:2023 02 04|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 3|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS3 RRBS3 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG3_L7_1.fq.gz CG3_L7_2.fq.gz fastq fastq 1164022500.0 3880075.0 CG3 L7 1.fq.gz 0:150 1:150 A:281490630;C:172929357;G:423757698;T:285795200;N:49615 150 150     281490630 172929357 423757698 285795200 49615 SRX23073958 SRS20033310 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0188 0.00046 0.01744 0.00039 0.99626 0.99981 0.55421 0.6 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29649 29649 SRR27397722 SRX23073957 SRS20033309 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library12 PG4   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 12|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS12 RRBS12 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG4_L7_1.fq.gz PG4_L7_2.fq.gz fastq fastq 937521000.0 3125070.0 PG4 L7 1.fq.gz 0:150 1:150 A:230277419;C:145742183;G:328432893;T:233027715;N:40790 150 150     230277419 145742183 328432893 233027715 40790 SRX23073957 SRS20033309 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01943 0.01926 0.01799 0.01786 0.99575 0.99588 0.51136 0.48062 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29650 29650 SRR27397723 SRX23073956 SRS20033308 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library11 PG3   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 11|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS11 RRBS11 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG3_L7_1.fq.gz PG3_L7_2.fq.gz fastq fastq 1256812500.0 4189375.0 PG3 L7 1.fq.gz 0:150 1:150 A:318736087;C:194540494;G:434374337;T:309107761;N:53821 150 150     318736087 194540494 434374337 309107761 53821 SRX23073956 SRS20033308 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01424 0.00046 0.01316 0.00036 0.99683 0.99975 0.49746 0.5 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29651 29651 SRR27397724 SRX23073955 SRS20033307 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library2 CG2   strain:ab|age:adult|collection date:2023 02 03|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 2|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS2 RRBS2 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG2_L7_1.fq.gz CG2_L7_2.fq.gz fastq fastq 1157888400.0 3859628.0 CG2 L7 1.fq.gz 0:150 1:150 A:292628434;C:171796176;G:406707172;T:286706357;N:50261 150 150     292628434 171796176 406707172 286706357 50261 SRX23073955 SRS20033307 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02036 0.02023 0.01903 0.01889 0.99616 0.99614 0.55102 0.57894 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29652 29652 SRR27397725 SRX23073954 SRS20033306 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library1 CG1   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 1|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS1 RRBS1 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG1_L7_1.fq.gz CG1_L7_2.fq.gz fastq fastq 1004867700.0 3349559.0 CG1 L7 1.fq.gz 0:150 1:150 A:247727849;C:158203386;G:350367173;T:248526527;N:42765 150 150     247727849 158203386 350367173 248526527 42765 SRX23073954 SRS20033306 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02764 0.00147 0.0252 0.00121 0.99233 0.99926 0.51541 0.5 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
66124 66124 SRR15927835 SRX12217977 SRS10194181 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate4   0.1MPa Muscle 4   strain:11|dev stage:adult|sex:female|tissue:Muscle|treatment:control|BioSampleModel:Model organism or animal                 0.1MPa Muscle 4 0.1MPa Muscle 4 0.1MPa Muscle 4 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     0.1MPa_Muscle_4_1.fq.gz 0.1MPa_Muscle_4_2.fq.gz fastq fastq 10711204800.0 35704016.0 0.1MPa Muscle 4 1.fq.gz 0:150 1:150 A:2765555622;C:2606137694;G:2609874691;T:2729600138;N:36655 150 150     2765555622 2606137694 2609874691 2729600138 36655 SRX12217977 SRS10194181 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.9603 0.95992 0.029 0.02943 0.79912 0.80044 0.51095 0.51424 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66127 66127 SRR15927793 SRX12217974 SRS10194177 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate3   0.1MPa Muscle 3   strain:10|dev stage:adult|sex:female|tissue:Muscle|treatment:control|BioSampleModel:Model organism or animal                 0.1MPa Muscle 3 0.1MPa Muscle 3 0.1MPa Muscle 3 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     0.1MPa_Muscle_3_1.fq.gz 0.1MPa_Muscle_3_2.fq.gz fastq fastq 9351747300.0 31172491.0 0.1MPa Muscle 3 1.fq.gz 0:150 1:150 A:2463095348;C:2227208452;G:2232723071;T:2428688760;N:31669 150 150     2463095348 2227208452 2232723071 2428688760 31669 SRX12217974 SRS10194177 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.95643 0.95498 0.04562 0.04593 0.77916 0.77944 0.51753 0.51578 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66128 66128 SRR15927794 SRX12217973 SRS10194176 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate2   0.1MPa Muscle 2   strain:9|dev stage:adult|sex:female|tissue:Muscle|treatment:control|BioSampleModel:Model organism or animal                 0.1MPa Muscle 2 0.1MPa Muscle 2 0.1MPa Muscle 2 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     0.1MPa_Muscle_2_1.fq.gz 0.1MPa_Muscle_2_2.fq.gz fastq fastq 11414630400.0 38048768.0 0.1MPa Muscle 2 1.fq.gz 0:150 1:150 A:2995912510;C:2724230960;G:2761157572;T:2933264368;N:64990 150 150     2995912510 2724230960 2761157572 2933264368 64990 SRX12217973 SRS10194176 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.96128 0.96023 0.02793 0.02781 0.82029 0.82016 0.50742 0.50638 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66129 66129 SRR15927795 SRX12217972 SRS10194175 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate1   0.1MPa Muscle 1   strain:8|dev stage:adult|sex:female|tissue:Muscle|treatment:control|BioSampleModel:Model organism or animal                 0.1MPa Muscle 1 0.1MPa Muscle 1 0.1MPa Muscle 1 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     0.1MPa_Muscle_1_1.fq.gz 0.1MPa_Muscle_1_2.fq.gz fastq fastq 15295642500.0 50985475.0 0.1MPa Muscle 1 1.fq.gz 0:150 1:150 A:3987711389;C:3692108838;G:3695351576;T:3920418318;N:52379 150 150     3987711389 3692108838 3695351576 3920418318 52379 SRX12217972 SRS10194175 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.95475 0.95466 0.03635 0.03693 0.7525 0.7542 0.51053 0.52086 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66136 66136 SRR15927802 SRX12217965 SRS10194168 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate4   9MPa Muscle 4   strain:41|dev stage:adult|sex:female|tissue:Muscle|treatment:9MPa4h|BioSampleModel:Model organism or animal                 9MPa Muscle 4 9MPa Muscle 4 9MPa Muscle 4 9MPa4h     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     9MPa_Muscle_4_1.fq.gz 9MPa_Muscle_4_2.fq.gz fastq fastq 6353225700.0 21177419.0 9MPa Muscle 4 1.fq.gz 0:150 1:150 A:1715999863;C:1474644800;G:1480968914;T:1681582526;N:29597 150 150     1715999863 1474644800 1480968914 1681582526 29597 SRX12217965 SRS10194168 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.96003 0.95939 0.0494 0.04931 0.82619 0.82641 0.55004 0.54769 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66138 66138 SRR15927804 SRX12217963 SRS10194166 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate3   9MPa Muscle 3   strain:40|dev stage:adult|sex:female|tissue:Muscle|treatment:9MPa4h|BioSampleModel:Model organism or animal                 9MPa Muscle 3 9MPa Muscle 3 9MPa Muscle 3 9MPa4h     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     9MPa_Muscle_3_1.fq.gz 9MPa_Muscle_3_2.fq.gz fastq fastq 6304419900.0 21014733.0 9MPa Muscle 3 1.fq.gz 0:150 1:150 A:1677572487;C:1489287765;G:1486352895;T:1651179933;N:26820 150 150     1677572487 1489287765 1486352895 1651179933 26820 SRX12217963 SRS10194166 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.96587 0.96598 0.04358 0.04311 0.81249 0.81282 0.4974 0.49616 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66139 66139 SRR15927805 SRX12217962 SRS10194164 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate2   9MPa Muscle 2   strain:39|dev stage:adult|sex:female|tissue:Muscle|treatment:9MPa4h|BioSampleModel:Model organism or animal                 9MPa Muscle 2 9MPa Muscle 2 9MPa Muscle 2 9MPa4h     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     9MPa_Muscle_2_1.fq.gz 9MPa_Muscle_2_2.fq.gz fastq fastq 6331644900.0 21105483.0 9MPa Muscle 2 1.fq.gz 0:150 1:150 A:1682942200;C:1496960626;G:1494865186;T:1656847825;N:29063 150 150     1682942200 1496960626 1494865186 1656847825 29063 SRX12217962 SRS10194164 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.96524 0.96513 0.03686 0.0365 0.80982 0.81154 0.54753 0.54898 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66140 66140 SRR15927806 SRX12217961 SRS10194163 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate1   9MPa Muscle 1   strain:38|dev stage:adult|sex:female|tissue:Muscle|treatment:9MPa4h|BioSampleModel:Model organism or animal                 9MPa Muscle 1 9MPa Muscle 1 9MPa Muscle 1 9MPa4h     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     9MPa_Muscle_1_1.fq.gz 9MPa_Muscle_1_2.fq.gz fastq fastq 6396622200.0 21322074.0 9MPa Muscle 1 1.fq.gz 0:150 1:150 A:1699778864;C:1511454865;G:1511402516;T:1673956561;N:29394 150 150     1699778864 1511454865 1511402516 1673956561 29394 SRX12217961 SRS10194163 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.96576 0.96563 0.04171 0.04097 0.79874 0.79902 0.47115 0.48566 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66153 66153 SRR15927819 SRX12217948 SRS10194150 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate4   5MPa Muscle 4   strain:26|dev stage:adult|sex:female|tissue:Muscle|treatment:5MPa4h|BioSampleModel:Model organism or animal                 5MPa Muscle 4 5MPa Muscle 4 5MPa Muscle 4 5MPa4h     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     5MPa_Muscle_4_1.fq.gz 5MPa_Muscle_4_2.fq.gz fastq fastq 6224364000.0 20747880.0 5MPa Muscle 4 1.fq.gz 0:150 1:150 A:1641927719;C:1481415127;G:1477217131;T:1623764097;N:39926 150 150     1641927719 1481415127 1477217131 1623764097 39926 SRX12217948 SRS10194150 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.96359 0.96348 0.04081 0.04097 0.81186 0.81189 0.48228 0.48384 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66154 66154 SRR15927820 SRX12217947 SRS10194149 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate3   5MPa Muscle 3   strain:25|dev stage:adult|sex:female|tissue:Muscle|treatment:5MPa4h|BioSampleModel:Model organism or animal                 5MPa Muscle 3 5MPa Muscle 3 5MPa Muscle 3 5MPa4h     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     5MPa_Muscle_3_1.fq.gz 5MPa_Muscle_3_2.fq.gz fastq fastq 6380934000.0 21269780.0 5MPa Muscle 3 1.fq.gz 0:150 1:150 A:1671974932;C:1532410091;G:1533693387;T:1642826090;N:29500 150 150     1671974932 1532410091 1533693387 1642826090 29500 SRX12217947 SRS10194149 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.96596 0.96544 0.04245 0.04209 0.81168 0.81345 0.52945 0.5252 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66155 66155 SRR15927821 SRX12217946 SRS10194148 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate2   5MPa Muscle 2   strain:24|dev stage:adult|sex:female|tissue:Muscle|treatment:5MPa4h|BioSampleModel:Model organism or animal                 5MPa Muscle 2 5MPa Muscle 2 5MPa Muscle 2 5MPa4h     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     5MPa_Muscle_2_1.fq.gz 5MPa_Muscle_2_2.fq.gz fastq fastq 6652238100.0 22174127.0 5MPa Muscle 2 1.fq.gz 0:150 1:150 A:1777745705;C:1559981557;G:1555946388;T:1758533051;N:31399 150 150     1777745705 1559981557 1555946388 1758533051 31399 SRX12217946 SRS10194148 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.95179 0.95144 0.05408 0.05364 0.71062 0.71127 0.52567 0.53034 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular System
66156 66156 SRR15927822 SRX12217945 SRS10194147 SRP337553 PRJNA764015 Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish PRJNA764015 Other the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure     replicate1   5MPa Muscle 1   strain:23|dev stage:adult|sex:female|tissue:Muscle|treatment:5MPa4h|BioSampleModel:Model organism or animal                 5MPa Muscle 1 5MPa Muscle 1 5MPa Muscle 1 5MPa4h     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP337553     5MPa_Muscle_1_1.fq.gz 5MPa_Muscle_1_2.fq.gz fastq fastq 6347703000.0 21159010.0 5MPa Muscle 1 1.fq.gz 0:150 1:150 A:1667447477;C:1517500269;G:1513605953;T:1649119009;N:30292 150 150     1667447477 1517500269 1513605953 1649119009 30292 SRX12217945 SRS10194147 SRA1295954 Northwestern Polytechnical University|School of Ecology and Environment Northwestern Polytechnical University 2 0.95624 0.95584 0.04626 0.04677 0.7413 0.74294 0.52854 0.52337 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-09-17 Adult Adult Muscle Muscular 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

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;