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run_metadata

22 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "Oligo-dT" and tissue_curation_coarse = "Embryo Imprecise"

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devstage_curation 4

experiment.platform 2

tissue_curation_coarse 1

  • Embryo Imprecise · 22 ✖

tissue_curation 1

technology 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 22 ✖

experiment.library_layout 1

  • SINGLE · 22 ✖

devstage_curation_coarse 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
9919 9919 ERR5167510 ERX4972431 ERS5593364 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     cDNA WT 2hpf rep1 JD T20 PDPN191089   ENA FIRST PUBLIC:2022 07 05T12:06:34Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:34Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05         ena RUN CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1                       ERX4972431   ERA3319053 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Cleavage Embryo Undetermined Embryo Imprecise
29719 29719 SRR27485664 SRX23156885 SRS20107306 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R3   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:3|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV06009 EV06009 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV06009.R1.fastq.gz fastq 809138488.0 10734286.0 EV06009.R1.fastq.gz 0:75.38 A:236901398;C:156814193;G:179647937;T:235732894;N:42066 75       236901398 156814193 179647937 235732894 42066 SRX23156885 SRS20107306 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.92159   0.07516   0.837   0.7566   69   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Undetermined Embryo Undetermined Embryo Imprecise
29730 29730 SRR27485675 SRX23156874 SRS20107295 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:2|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV06002 EV06002 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV06002.R1.fastq.gz fastq 632849068.0 8404028.0 EV06002.R1.fastq.gz 0:75.30 A:194183801;C:123105421;G:139266843;T:176255048;N:37955 75       194183801 123105421 139266843 176255048 37955 SRX23156874 SRS20107295 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.88896   0.09385   0.81864   0.73385   75   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Undetermined Embryo Undetermined Embryo Imprecise
29737 29737 SRR27477297 SRX23148650 SRS20099368 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:4|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV09002 EV09002 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV09002.R1.fastq.gz fastq 546999929.0 7270092.0 EV09002.R1.fastq.gz 0:75.24 A:165415993;C:110874896;G:124384517;T:146294099;N:30424 75       165415993 110874896 124384517 146294099 30424 SRX23148650 SRS20099368 SRA1782413 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.9065   0.11883   0.82231   0.74466   75   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-10 Undetermined Embryo Undetermined Embryo Imprecise
60104 60104 SRR12142045 SRX8663215 SRS6944340 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 4   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 4 Dre 4 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g004_1.fastq.gz fastq 509713380.0 9994380.0 DreSceMix g004 1.fastq.gz 0:51 A:251366594;C:61585710;G:62159129;T:134578953;N:22994 51       251366594 61585710 62159129 134578953 22994 SRX8663215 SRS6944340 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.67392   0.54102   0.86476   0.37091   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60105 60105 SRR12141709 SRX8663075 SRS6944200 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 3   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 3 Dre 3 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g003_1.fastq.gz fastq 499717482.0 9798382.0 DreSceMix g003 1.fastq.gz 0:51 A:263221073;C:56114768;G:56547079;T:123812019;N:22543 51       263221073 56114768 56547079 123812019 22543 SRX8663075 SRS6944200 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.63258   0.48288   0.86819   0.35874   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60106 60106 SRR12141808 SRX8662976 SRS6944101 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 6   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 12 Dre 12 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g014_1.fastq.gz fastq 421063599.0 8256149.0 DreSceMix g014 1.fastq.gz 0:51 A:207118237;C:53600213;G:54041718;T:106284709;N:18722 51       207118237 53600213 54041718 106284709 18722 SRX8662976 SRS6944101 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.47999   0.19308   0.85977   0.46733   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60107 60107 SRR12141828 SRX8662956 SRS6944081 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 4   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 10 Dre 10 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g012_1.fastq.gz fastq 626464773.0 12283623.0 DreSceMix g012 1.fastq.gz 0:51 A:263307070;C:96744908;G:98635228;T:167749896;N:27671 51       263307070 96744908 98635228 167749896 27671 SRX8662956 SRS6944081 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.50608   0.14369   0.83422   0.45691   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60108 60108 SRR12141839 SRX8662945 SRS6944070 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 3   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 9 Dre 9 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g011_1.fastq.gz fastq 436381296.0 8556496.0 DreSceMix g011 1.fastq.gz 0:51 A:205579619;C:58008903;G:59021026;T:113752218;N:19530 51       205579619 58008903 59021026 113752218 19530 SRX8662945 SRS6944070 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.46615   0.18281   0.84778   0.44592   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60109 60109 SRR12141850 SRX8662934 SRS6944059 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 2   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 8 Dre 8 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g010_1.fastq.gz fastq 870727437.0 17073087.0 DreSceMix g010 1.fastq.gz 0:51 A:343772776;C:142428987;G:145570260;T:238917135;N:38279 51       343772776 142428987 145570260 238917135 38279 SRX8662934 SRS6944059 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.52883   0.1235   0.82256   0.45498   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60110 60110 SRR12141861 SRX8662923 SRS6944047 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 1   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 7 Dre 7 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g009_1.fastq.gz fastq 1875928206.0 36782906.0 DreSceMix g009 1.fastq.gz 0:51 A:684015713;C:329272255;G:335557540;T:526999083;N:83615 51       684015713 329272255 335557540 526999083 83615 SRX8662923 SRS6944047 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.58553   0.11315   0.8029   0.4678   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60111 60111 SRR12141872 SRX8662912 SRS6944037 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 6   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 6 Dre 6 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g006_1.fastq.gz fastq 390346044.0 7653844.0 DreSceMix g006 1.fastq.gz 0:51 A:194005234;C:46666192;G:46964771;T:102692143;N:17704 51       194005234 46666192 46964771 102692143 17704 SRX8662912 SRS6944037 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.69496   0.57077   0.86864   0.35451   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60112 60112 SRR12141959 SRX8662825 SRS6943950 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 5   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 5 Dre 5 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g005_1.fastq.gz fastq 684050964.0 13412764.0 DreSceMix g005 1.fastq.gz 0:51 A:318875237;C:88359396;G:89394558;T:187391266;N:30507 51       318875237 88359396 89394558 187391266 30507 SRX8662825 SRS6943950 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.61659   0.4142   0.8393   0.42049   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60113 60113 SRR12142001 SRX8662783 SRS6943908 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 5   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 11 Dre 11 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g013_1.fastq.gz fastq 998754318.0 19583418.0 DreSceMix g013 1.fastq.gz 0:51 A:402091762;C:156702863;G:160047354;T:279867921;N:44418 51       402091762 156702863 160047354 279867921 44418 SRX8662783 SRS6943908 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.52766   0.13651   0.81237   0.45557   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60114 60114 SRR12142002 SRX8662782 SRS6943907 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 2   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 2 Dre 2 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g002_1.fastq.gz fastq 702610578.0 13776678.0 DreSceMix g002 1.fastq.gz 0:51 A:332485038;C:89482705;G:90437771;T:190173083;N:31981 51       332485038 89482705 90437771 190173083 31981 SRX8662782 SRS6943907 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.63597   0.45832   0.85088   0.40969   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60115 60115 SRR12142003 SRX8662781 SRS6943906 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 1   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 1 Dre 1 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g001_1.fastq.gz fastq 1273185777.0 24964427.0 DreSceMix g001 1.fastq.gz 0:51 A:541573299;C:186989405;G:191401487;T:353163815;N:57771 51       541573299 186989405 191401487 353163815 57771 SRX8662781 SRS6943906 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.62046   0.30937   0.8197   0.44014   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
69604 69604 SRR18935955 SRX15013551 SRS12762156 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alad RBC   strain:alad mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81332 L81332 FACS sorted alad mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alad-2_L7_I332.R1.clean.fastq.gz fastq 3448675800.0 22991172.0 Alad 2 L7 I332.R1.clean.fastq.gz 0:150 1:0 A:909204217;C:819708757;G:815883274;T:903292138;N:587414 150 0     909204217 819708757 815883274 903292138 587414 SRX15013551 SRS12762156 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.93973   0.13997   0.7685   0.51168   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69605 69605 SRR18935956 SRX15013550 SRS12762156 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alad RBC   strain:alad mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81331 L81331 FACS sorted alad mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alad-1_L8_I331.R1.clean.fastq.gz fastq 3987610500.0 26584070.0 Alad 1 L8 I331.R1.clean.fastq.gz 0:150 1:0 A:1031398922;C:974521107;G:967367126;T:1013951504;N:371841 150 0     1031398922 974521107 967367126 1013951504 371841 SRX15013550 SRS12762156 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.9447   0.1019   0.81286   0.58316   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69606 69606 SRR18935957 SRX15013549 SRS12762155 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alas2 RBC   strain:alas2 mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81330 L81330 FACS sorted alas2 mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alas2-2_L8_I330.R1.clean.fastq.gz fastq 4163915100.0 27759434.0 Alas2 2 L8 I330.R1.clean.fastq.gz 0:150 1:0 A:1119245849;C:968636914;G:967111308;T:1108544148;N:376881 150 0     1119245849 968636914 967111308 1108544148 376881 SRX15013549 SRS12762155 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.92608   0.1778   0.75471   0.55161   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69607 69607 SRR18935958 SRX15013548 SRS12762155 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alas2 RBC   strain:alas2 mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81329 L81329 FACS sorted alas2 mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alas2-1_L8_I329.R1.clean.fastq.gz fastq 3953391150.0 26355941.0 Alas2 1 L8 I329.R1.clean.fastq.gz 0:150 1:0 A:1035309566;C:950958591;G:946245209;T:1020520823;N:356961 150 0     1035309566 950958591 946245209 1020520823 356961 SRX15013548 SRS12762155 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.93024   0.14212   0.81213   0.61442   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69608 69608 SRR18935959 SRX15013547 SRS12762154 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         WT RBC   strain:WT|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81328 L81328 FACS sorted WT RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     WT-2_L8_I328.R1.clean.fastq.gz fastq 3589015200.0 23926768.0 WT 2 L8 I328.R1.clean.fastq.gz 0:150 1:0 A:922300230;C:887849832;G:879590696;T:898942142;N:332300 150 0     922300230 887849832 879590696 898942142 332300 SRX15013547 SRS12762154 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.94576   0.09241   0.83514   0.68592   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69609 69609 SRR18935960 SRX15013546 SRS12762154 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         WT RBC   strain:WT|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81327 L81327 FACS sorted WT RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     WT-1_L8_I327.R1.clean.fastq.gz fastq 4062851700.0 27085678.0 WT 1 L8 I327.R1.clean.fastq.gz 0:150 1:0 A:1028410873;C:1020911876;G:1010215515;T:1002940085;N:373351 150 0     1028410873 1020911876 1010215515 1002940085 373351 SRX15013546 SRS12762154 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.94919   0.0692   0.85567   0.70156   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise

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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");;