run_metadata
94 rows where devstage_curation_coarse = "Undetermined" and experiment.library_selection = "Oligo-dT"
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| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9918 | 9918 | ERR5059480 | ERX4865549 | ERS5523939 | 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 | aAM 6h rep1 | JD AD30 PRPN1970901 | ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|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 09 01 2021 19:50:56:183 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 | JD-AD30_PRPN197090.tar.gz | nanopore | 3739882337.0 | 3148027.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 | 0:1188.01 | A:1054501690;C:834193435;G:847423060;T:1003764152;N:0 | 1188 | 1054501690 | 834193435 | 847423060 | 1003764152 | 0 | ERX4865549 | ERS5523939 | ERA3206712 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | B | usable mapping rate | ont | ont | unknown | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-07-05 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||||||||||||||||||||
| 9920 | 9920 | ERR4330695 | ERX4277529 | ERS4811113 | 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 | WT 2h rep1 | WT 2h rep1 | SAMEA7050483 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727 | PromethION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 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 | JD-B2_PDBN005727.tar.gz | fastq | ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1 | ERX4277529 | ERA2767154 | 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 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||||||||||||||||
| 9921 | 9921 | ERR4327134 | ERX4273968 | ERS4808634 | 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 | WT 4h rep2 | WT 4h rep2 | SAMEA7048000 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841 | PromethION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 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 | JD-AM39_PDBN042841.tar.gz | nanopore | 719646261.0 | 897768.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 | 0:801.59 | A:210217908;C:152963718;G:157393834;T:199070801;N:0 | 801 | 210217908 | 152963718 | 157393834 | 199070801 | 0 | ERX4273968 | ERS4808634 | ERA2764800 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | T | under 1.2% mapping rate | ont | ont | unknown | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-07-05 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||||||||||||||||||
| 9922 | 9922 | ERR4330696 | ERX4277530 | ERS4811114 | 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 | WT 4h rep1 | WT 4h rep1 | JD C3 PDBN006177 | ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|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 09 07 2020 13:48:01:100 2 | 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 | JD-C3_PDBN006177.tar.gz | nanopore | 4240799932.0 | 4331689.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 | 0:979.02 | A:1229803846;C:914476674;G:943703560;T:1152815852;N:0 | 979 | 1229803846 | 914476674 | 943703560 | 1152815852 | 0 | ERX4277530 | ERS4811114 | ERA2767154 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | B | usable mapping rate | ont | ont | unknown | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-07-05 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||||
| 9923 | 9923 | ERR4327135 | ERX4273969 | ERS4808635 | 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 | WT 6h rep1 | WT 6h rep1 | JD AC29 PDBN024889 | ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|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 07 07 2020 16:36:02:084 2 | 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 | JD-AC29_PDBN024889.tar.gz | nanopore | 1900324756.0 | 2013035.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 | 0:944.01 | A:549431032;C:411510218;G:422103800;T:517279706;N:0 | 944 | 549431032 | 411510218 | 422103800 | 517279706 | 0 | ERX4273969 | ERS4808635 | ERA2764800 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | T | long read | ont | ont | unknown | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-07-05 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||||
| 9924 | 9924 | ERR4326350 | ERX4273208 | ERS4808398 | 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 | 430 LNA 6h rep1 | 430 LNA 6h rep1 | SAMEA7047764 | CENTER FOR GENOMIC REGULATION (CRG) | ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569 | PromethION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 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 | JD-H8_PDBN059569.tar.gz | nanopore | 722817654.0 | 657296.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 | 0:1099.68 | A:206996491;C:157022109;G:155085437;T:203713617;N:0 | 1099 | 206996491 | 157022109 | 155085437 | 203713617 | 0 | ERX4273208 | ERS4808398 | ERA2764399 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | T | under 1.2% mapping rate | ont | ont | unknown | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-07-05 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||||||||||||||||||
| 9925 | 9925 | ERR4335436 | ERX4282181 | ERS4818366 | 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 | WT 6h rep2 | WT 6h rep2 | JD W23 PRPN039928 | ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|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 13 07 2020 18:19:23:456 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 | JD-W23_PRPN039928.tar.gz | nanopore | 1268761319.0 | 1385621.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1 | 0:915.66 | A:366823862;C:275507684;G:284634548;T:341795225;N:0 | 915 | 366823862 | 275507684 | 284634548 | 341795225 | 0 | ERX4282181 | ERS4818366 | ERA2769006 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | T | under 1.2% mapping rate | ont | ont | unknown | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-07-05 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||||
| 9926 | 9926 | ERR4321680 | ERX4268538 | ERS4808125 | 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 | WT 0h rep1 | WT 0h rep1 | JD A1 GDDN003032 | ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 | GridION sequencing | ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | OXFORD_NANOPORE | GridION | ERP122761 | GridION sequencing | ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 | JD-A1_GDDN003032.tar.gz | nanopore | 753417826.0 | 698774.0 | ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 | 0:1078.20 | A:214525685;C:165042952;G:171160615;T:202688574;N:0 | 1078 | 214525685 | 165042952 | 171160615 | 202688574 | 0 | ERX4268538 | ERS4808125 | ERA2763718 | CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive | CENTER FOR GENOMIC REGULATION (CRG) | T | long read | ont | ont | unknown | poly_a | unknown | bulk | unknown | unknown | Spain | 2022-07-05 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||||
| 11143 | 11143 | ERR10034092 | ERX9574496 | ERS12562207 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Postmetamorphic posterior tissue including caudal fin from Danio rerio | Drerio postmetamorphic 5 | SAMEA110464179 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464179|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE45|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE45|sex:not provided|tissue type:posterior trunk including caudal fin | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:841 19218 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr45.1.fastq.gz S879Nr45.2.fastq.gz | fastq fastq | 31205725028.0 | 155856846.0 | ena RUN TAB 05 08 2022 14:25:08:841 19219 | 0:100.11 1:100.11 | A:8165930827;C:7529482042;G:7775787815;T:7734109822;N:414522 | 100 | 100 | 8165930827 | 7529482042 | 7775787815 | 7734109822 | 414522 | ERX9574496 | ERS12562207 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.97305 | 0.97331 | 0.04336 | 0.04353 | 0.73728 | 0.74324 | 0.47532 | 0.4806 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Multi-tissue | Multi-system | ||||||||||||||
| 11144 | 11144 | ERR10034091 | ERX9574495 | ERS12562206 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Postmetamorphic posterior tissue including caudal fin from Danio rerio | Drerio postmetamorphic 4 | SAMEA110464178 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464178|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE44|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE44|sex:not provided|tissue type:posterior trunk including caudal fin | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:841 19216 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr44.1.fastq.gz S879Nr44.2.fastq.gz | fastq fastq | 12791868714.0 | 63868301.0 | ena RUN TAB 05 08 2022 14:25:08:841 19217 | 0:100.14 1:100.14 | A:3327645062;C:3095411506;G:3211023712;T:3157616450;N:171984 | 100 | 100 | 3327645062 | 3095411506 | 3211023712 | 3157616450 | 171984 | ERX9574495 | ERS12562206 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.97212 | 0.97067 | 0.04428 | 0.04445 | 0.74548 | 0.75114 | 0.47785 | 0.49354 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Multi-tissue | Multi-system | ||||||||||||||
| 11145 | 11145 | ERR10034090 | ERX9574494 | ERS12562205 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Postmetamorphic posterior tissue including caudal fin from Danio rerio | Drerio postmetamorphic 3 | SAMEA110464177 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464177|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE43|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE43|sex:not provided|tissue type:posterior trunk including caudal fin | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19214 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr43.1.fastq.gz S879Nr43.2.fastq.gz | fastq fastq | 8220676412.0 | 40976395.0 | ena RUN TAB 05 08 2022 14:25:08:840 19215 | 0:100.31 1:100.31 | A:2152497687;C:1985765652;G:2020897890;T:2061403084;N:112099 | 100 | 100 | 2152497687 | 1985765652 | 2020897890 | 2061403084 | 112099 | ERX9574494 | ERS12562205 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.97126 | 0.97279 | 0.04717 | 0.04683 | 0.74223 | 0.74479 | 0.47471 | 0.49071 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Multi-tissue | Multi-system | ||||||||||||||
| 11146 | 11146 | ERR10034089 | ERX9574493 | ERS12562204 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Postmetamorphic posterior tissue including caudal fin from Danio rerio | Drerio postmetamorphic 2 | SAMEA110464176 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464176|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE42|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE42|sex:not provided|tissue type:posterior trunk including caudal fin | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19212 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr42.1.fastq.gz S879Nr42.2.fastq.gz | fastq fastq | 9426020714.0 | 47021406.0 | ena RUN TAB 05 08 2022 14:25:08:840 19213 | 0:100.23 1:100.23 | A:2487913802;C:2263414842;G:2331327650;T:2343237033;N:127387 | 100 | 100 | 2487913802 | 2263414842 | 2331327650 | 2343237033 | 127387 | ERX9574493 | ERS12562204 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.97197 | 0.97222 | 0.04546 | 0.04553 | 0.74235 | 0.7485 | 0.48841 | 0.48446 | 93 | 93 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Multi-tissue | Multi-system | ||||||||||||||
| 11147 | 11147 | ERR10034088 | ERX9574492 | ERS12562203 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Postmetamorphic posterior tissue including caudal fin from Danio rerio | Drerio postmetamorphic 1 | SAMEA110464175 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464175|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE41|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE41|sex:not provided|tissue type:posterior trunk including caudal fin | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19210 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr41.1.fastq.gz S879Nr41.2.fastq.gz | fastq fastq | 10220995994.0 | 50953819.0 | ena RUN TAB 05 08 2022 14:25:08:840 19211 | 0:100.30 1:100.30 | A:2679378092;C:2474435843;G:2537496182;T:2529546220;N:139657 | 100 | 100 | 2679378092 | 2474435843 | 2537496182 | 2529546220 | 139657 | ERX9574492 | ERS12562203 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.97322 | 0.97339 | 0.05421 | 0.05374 | 0.73693 | 0.74194 | 0.50642 | 0.50631 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Multi-tissue | Multi-system | ||||||||||||||
| 11148 | 11148 | ERR10034072 | ERX9574476 | ERS12562187 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Metamorphic tissue without xxx from Danio rerio | Drerio metamorphic 5 | SAMEA110464159 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464159|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE25|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE25|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19178 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr25.1.fastq.gz S879Nr25.2.fastq.gz | fastq fastq | 10120435126.0 | 50403985.0 | ena RUN TAB 05 08 2022 14:25:08:835 19179 | 0:100.39 1:100.39 | A:2679131890;C:2420708190;G:2483153503;T:2537307238;N:134305 | 100 | 100 | 2679131890 | 2420708190 | 2483153503 | 2537307238 | 134305 | ERX9574476 | ERS12562187 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.96973 | 0.97106 | 0.04979 | 0.04949 | 0.71252 | 0.71654 | 0.4806 | 0.49338 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Trunk | Surface Structure | ||||||||||||||
| 11149 | 11149 | ERR10034071 | ERX9574475 | ERS12562186 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Metamorphic tissue without xxx from Danio rerio | Drerio metamorphic 4 | SAMEA110464158 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464158|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE24|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE24|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19176 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr24.1.fastq.gz S879Nr24.2.fastq.gz | fastq fastq | 7845661906.0 | 39121993.0 | ena RUN TAB 05 08 2022 14:25:08:835 19177 | 0:100.27 1:100.27 | A:2096079479;C:1862247618;G:1929220494;T:1958006859;N:107456 | 100 | 100 | 2096079479 | 1862247618 | 1929220494 | 1958006859 | 107456 | ERX9574475 | ERS12562186 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.96989 | 0.96986 | 0.04901 | 0.04902 | 0.71599 | 0.72301 | 0.48965 | 0.48827 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Trunk | Surface Structure | ||||||||||||||
| 11150 | 11150 | ERR10034070 | ERX9574474 | ERS12562185 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Metamorphic tissue without xxx from Danio rerio | Drerio metamorphic 3 | SAMEA110464157 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464157|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE23|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE23|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19174 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr23.1.fastq.gz S879Nr23.2.fastq.gz | fastq fastq | 8270390422.0 | 41338131.0 | ena RUN TAB 05 08 2022 14:25:08:835 19175 | 0:100.03 1:100.03 | A:2156060704;C:1998612686;G:2055201244;T:2060404840;N:110948 | 100 | 100 | 2156060704 | 1998612686 | 2055201244 | 2060404840 | 110948 | ERX9574474 | ERS12562185 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.97085 | 0.97083 | 0.04232 | 0.04236 | 0.7219 | 0.72671 | 0.47325 | 0.4807 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Trunk | Surface Structure | ||||||||||||||
| 11151 | 11151 | ERR10034069 | ERX9574473 | ERS12562184 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Metamorphic tissue without xxx from Danio rerio | Drerio metamorphic 2 | SAMEA110464156 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464156|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE22|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE22|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19172 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr22.1.fastq.gz S879Nr22.2.fastq.gz | fastq fastq | 10977356920.0 | 54380062.0 | ena RUN TAB 05 08 2022 14:25:08:834 19173 | 0:100.93 1:100.93 | A:2852856166;C:2671616791;G:2798184312;T:2654546853;N:152798 | 100 | 100 | 2852856166 | 2671616791 | 2798184312 | 2654546853 | 152798 | ERX9574473 | ERS12562184 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.9765 | 0.97629 | 0.03531 | 0.03529 | 0.72025 | 0.72705 | 0.47808 | 0.46326 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Trunk | Surface Structure | ||||||||||||||
| 11152 | 11152 | ERR10034068 | ERX9574472 | ERS12562183 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Metamorphic tissue without xxx from Danio rerio | Drerio metamorphic 1 | SAMEA110464155 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464155|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE21|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE21|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19170 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr21.1.fastq.gz S879Nr21.2.fastq.gz | fastq fastq | 11346084502.0 | 56210802.0 | ena RUN TAB 05 08 2022 14:25:08:834 19171 | 0:100.92 1:100.92 | A:2950787998;C:2755514202;G:2902131288;T:2737495846;N:155168 | 100 | 100 | 2950787998 | 2755514202 | 2902131288 | 2737495846 | 155168 | ERX9574472 | ERS12562183 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.9732 | 0.97208 | 0.02959 | 0.02983 | 0.72322 | 0.73135 | 0.47796 | 0.47326 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Undetermined | Undetermined | Trunk | Surface Structure | ||||||||||||||
| 24918 | 24918 | SRR25594442 | SRX21322829 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | Z 2 1.fq | Z 2 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | Z-2_2.fq.gz Z-2_1.fq.gz | fastq fastq | 5621492400.0 | 18738308.0 | Z 2 1.fq.gz | 0:150 1:150 | A:1483421677;C:1306378425;G:1338052121;T:1493618330;N:21847 | 150 | 150 | 1483421677 | 1306378425 | 1338052121 | 1493618330 | 21847 | SRX21322829 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.94389 | 0.93819 | 0.03702 | 0.03621 | 0.71758 | 0.72423 | 0.43774 | 0.4558 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 24919 | 24919 | SRR25594443 | SRX21322828 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | Z 1 1.fq | Z 1 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | Z-1_2.fq.gz Z-1_1.fq.gz | fastq fastq | 6301274700.0 | 21004249.0 | Z 1 1.fq.gz | 0:150 1:150 | A:1671253253;C:1458678359;G:1491311308;T:1680006330;N:25450 | 150 | 150 | 1671253253 | 1458678359 | 1491311308 | 1680006330 | 25450 | SRX21322828 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.94339 | 0.93817 | 0.03831 | 0.03813 | 0.71752 | 0.72293 | 0.42611 | 0.43548 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 24920 | 24920 | SRR25594444 | SRX21322827 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | K 3 1.fq | K 3 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | K-3_2.fq.gz K-3_1.fq.gz | fastq fastq | 5519682000.0 | 18398940.0 | K 3 1.fq.gz | 0:150 1:150 | A:1469946965;C:1270791684;G:1304075220;T:1474846842;N:21289 | 150 | 150 | 1469946965 | 1270791684 | 1304075220 | 1474846842 | 21289 | SRX21322827 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.94356 | 0.93561 | 0.03986 | 0.03923 | 0.71877 | 0.72697 | 0.44771 | 0.44936 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 24921 | 24921 | SRR25594445 | SRX21322826 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | K 2 1.fq | K 2 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | K-2_1.fq.gz K-2_2.fq.gz | fastq fastq | 5808261300.0 | 19360871.0 | K 2 1.fq.gz | 0:150 1:150 | A:1538012312;C:1343217111;G:1375887577;T:1551118640;N:25660 | 150 | 150 | 1538012312 | 1343217111 | 1375887577 | 1551118640 | 25660 | SRX21322826 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.94469 | 0.94137 | 0.03929 | 0.03857 | 0.7175 | 0.71946 | 0.44395 | 0.44354 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 24922 | 24922 | SRR25594446 | SRX21322825 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | ZP 3 1.fq | ZP 3 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | ZP-3_1.fq.gz ZP-3_2.fq.gz | fastq fastq | 5397938100.0 | 17993127.0 | ZP 3 1.fq.gz | 0:150 1:150 | A:1438191584;C:1244532731;G:1271700792;T:1443491138;N:21855 | 150 | 150 | 1438191584 | 1244532731 | 1271700792 | 1443491138 | 21855 | SRX21322825 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.94839 | 0.94406 | 0.04345 | 0.04279 | 0.71719 | 0.72362 | 0.42772 | 0.4311 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 24923 | 24923 | SRR25594447 | SRX21322824 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | ZP 2 1.fq | ZP 2 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | ZP-2_1.fq.gz ZP-2_2.fq.gz | fastq fastq | 6062424900.0 | 20208083.0 | ZP 2 1.fq.gz | 0:150 1:150 | A:1612595576;C:1398589726;G:1427536119;T:1623678727;N:24752 | 150 | 150 | 1612595576 | 1398589726 | 1427536119 | 1623678727 | 24752 | SRX21322824 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.95013 | 0.94657 | 0.04364 | 0.04342 | 0.71565 | 0.71908 | 0.44652 | 0.44832 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 24924 | 24924 | SRR25594448 | SRX21322823 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | ZP 1 1.fq | ZP 1 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | ZP-1_2.fq.gz ZP-1_1.fq.gz | fastq fastq | 6487607100.0 | 21625357.0 | ZP 1 1.fq.gz | 0:150 1:150 | A:1728514584;C:1494175744;G:1521726756;T:1743164500;N:25516 | 150 | 150 | 1728514584 | 1494175744 | 1521726756 | 1743164500 | 25516 | SRX21322823 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.94867 | 0.94432 | 0.04535 | 0.0449 | 0.71926 | 0.72348 | 0.43747 | 0.44661 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 24925 | 24925 | SRR25594449 | SRX21322822 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | Z 3 1.fq | Z 3 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | Z-3_1.fq.gz Z-3_2.fq.gz | fastq fastq | 8111204700.0 | 27037349.0 | Z 3 1.fq.gz | 0:150 1:150 | A:2143712842;C:1879826122;G:1918517283;T:2169119328;N:29125 | 150 | 150 | 2143712842 | 1879826122 | 1918517283 | 2169119328 | 29125 | SRX21322822 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.94485 | 0.94083 | 0.03886 | 0.03798 | 0.71362 | 0.71768 | 0.44066 | 0.44713 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 24926 | 24926 | SRR25594450 | SRX21322821 | SRS18569855 | SRP454395 | PRJNA1002816 | Danio rerio Raw sequence reads | PRJNA1002816 | Whole Genome Sequencing | Zebrafish Transcriptome | Zebrafish intestine | strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal | Zebrafish Intestinal Transcriptome | K 1 1.fq | K 1 1.fq | Intestinal Transcriptome | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP454395 | K-1_1.fq.gz K-1_2.fq.gz | fastq fastq | 7164142200.0 | 23880474.0 | K 1 1.fq.gz | 0:150 1:150 | A:1896647470;C:1661542391;G:1700422400;T:1905500150;N:29789 | 150 | 150 | 1896647470 | 1661542391 | 1700422400 | 1905500150 | 29789 | SRX21322821 | SRS18569855 | SRA1689922 | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish | Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences | 2 | 0.94635 | 0.94209 | 0.03738 | 0.03664 | 0.71961 | 0.72571 | 0.45014 | 0.44857 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-08-10 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 28458 | 28458 | SRR26265233 | SRX21974767 | SRS19050630 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | IFN4 2 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 10|BioSampleModel:Model organism or animal | RNAseq of zebrafish | IFND2 | IFND2 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | IFN4-2.R2.fq.gz IFN4-2.R1.fq.gz | fastq fastq | 6934783900.0 | 23533465.0 | IFN4 2.R1.fq.gz | 0:147.35 1:147.33 | A:1868083790;C:1590902416;G:1598661179;T:1876555558;N:580957 | 147 | 147 | 1868083790 | 1590902416 | 1598661179 | 1876555558 | 580957 | SRX21974767 | SRS19050630 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95226 | 0.95256 | 0.09237 | 0.09199 | 0.73403 | 0.73472 | 0.50112 | 0.4946 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28459 | 28459 | SRR26265234 | SRX21974766 | SRS19050629 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | IFN4 1 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 9|BioSampleModel:Model organism or animal | RNAseq of zebrafish | IFND1 | IFND1 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | IFN4-1.R2.fq.gz IFN4-1.R1.fq.gz | fastq fastq | 6955503146.0 | 23557276.0 | IFN4 1.R1.fq.gz | 0:147.65 1:147.61 | A:1873984869;C:1595727817;G:1603714470;T:1881209728;N:866262 | 147 | 147 | 1873984869 | 1595727817 | 1603714470 | 1881209728 | 866262 | SRX21974766 | SRS19050629 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95329 | 0.95472 | 0.09371 | 0.09311 | 0.73535 | 0.7362 | 0.49542 | 0.49872 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28460 | 28460 | SRR26265235 | SRX21974765 | SRS19050628 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | IFN1 4 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 8|BioSampleModel:Model organism or animal | RNAseq of zebrafish | IFNA4 | IFNA4 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | IFN1-4.R1.fq.gz IFN1-4.R2.fq.gz | fastq fastq | 6497442039.0 | 22025966.0 | IFN1 4.R1.fq.gz | 0:147.50 1:147.49 | A:1752434033;C:1488528327;G:1495225910;T:1760699235;N:554534 | 147 | 147 | 1752434033 | 1488528327 | 1495225910 | 1760699235 | 554534 | SRX21974765 | SRS19050628 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95168 | 0.95288 | 0.09073 | 0.09058 | 0.73691 | 0.73697 | 0.49659 | 0.49706 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28461 | 28461 | SRR26265236 | SRX21974764 | SRS19050627 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | IFN1 3 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 7|BioSampleModel:Model organism or animal | RNAseq of zebrafish | IFNA3 | IFNA3 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | IFN1-3.R1.fq.gz IFN1-3.R2.fq.gz | fastq fastq | 6258791362.0 | 21164255.0 | IFN1 3.R1.fq.gz | 0:147.88 1:147.85 | A:1687323085;C:1434335716;G:1441365307;T:1695236268;N:530986 | 147 | 147 | 1687323085 | 1434335716 | 1441365307 | 1695236268 | 530986 | SRX21974764 | SRS19050627 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95206 | 0.95262 | 0.09255 | 0.09194 | 0.73549 | 0.73503 | 0.49685 | 0.50433 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28462 | 28462 | SRR26265237 | SRX21974763 | SRS19050626 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | IFN1 2 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 6|BioSampleModel:Model organism or animal | RNAseq of zebrafish | IFNA2 | IFNA2 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | IFN1-2.R1.fq.gz IFN1-2.R2.fq.gz | fastq fastq | 5566110483.0 | 18875664.0 | IFN1 2.R1.fq.gz | 0:147.46 1:147.43 | A:1498457518;C:1278011392;G:1284254482;T:1504942516;N:444575 | 147 | 147 | 1498457518 | 1278011392 | 1284254482 | 1504942516 | 444575 | SRX21974763 | SRS19050626 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95197 | 0.9524 | 0.09035 | 0.08962 | 0.73606 | 0.73634 | 0.50146 | 0.49994 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28463 | 28463 | SRR26265238 | SRX21974762 | SRS19050625 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | IFN1 1 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 5|BioSampleModel:Model organism or animal | RNAseq of zebrafish | IFNA1 | IFNA1 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | IFN1-1.R1.fq.gz IFN1-1.R2.fq.gz | fastq fastq | 6919610192.0 | 23425305.0 | IFN1 1.R1.fq.gz | 0:147.71 1:147.68 | A:1863998722;C:1587286271;G:1595557648;T:1872190552;N:576999 | 147 | 147 | 1863998722 | 1587286271 | 1595557648 | 1872190552 | 576999 | SRX21974762 | SRS19050625 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95297 | 0.95392 | 0.08926 | 0.0886 | 0.73744 | 0.73716 | 0.48737 | 0.49536 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28464 | 28464 | SRR26265239 | SRX21974761 | SRS19050624 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | Control 4 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 4|BioSampleModel:Model organism or animal | RNAseq of zebrafish | C4 | C4 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | Control-4.R1.fq.gz Control-4.R2.fq.gz | fastq fastq | 7048754711.0 | 23843338.0 | Control 4.R1.fq.gz | 0:147.83 1:147.80 | A:1886695953;C:1629137936;G:1637672845;T:1894536437;N:711540 | 147 | 147 | 1886695953 | 1629137936 | 1637672845 | 1894536437 | 711540 | SRX21974761 | SRS19050624 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.9556 | 0.95723 | 0.09014 | 0.08984 | 0.73533 | 0.73643 | 0.50146 | 0.50134 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28465 | 28465 | SRR26265240 | SRX21974760 | SRS19050623 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | Control 3 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 3|BioSampleModel:Model organism or animal | RNAseq of zebrafish | C3 | C3 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | Control-3.R1.fq.gz Control-3.R2.fq.gz | fastq fastq | 6936430397.0 | 23495179.0 | Control 3.R1.fq.gz | 0:147.63 1:147.60 | A:1861679698;C:1598594022;G:1606747561;T:1868699697;N:709419 | 147 | 147 | 1861679698 | 1598594022 | 1606747561 | 1868699697 | 709419 | SRX21974760 | SRS19050623 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95496 | 0.95472 | 0.09092 | 0.08958 | 0.73505 | 0.73586 | 0.50541 | 0.50256 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28466 | 28466 | SRR26265241 | SRX21974759 | SRS19050622 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | IFN4 4 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 12|BioSampleModel:Model organism or animal | RNAseq of zebrafish | IFND4 | IFND4 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | IFN4-4.R1.fq.gz IFN4-4.R2.fq.gz | fastq fastq | 6904025687.0 | 23391394.0 | IFN4 4.R1.fq.gz | 0:147.59 1:147.56 | A:1858866141;C:1585020535;G:1592940944;T:1866550686;N:647381 | 147 | 147 | 1858866141 | 1585020535 | 1592940944 | 1866550686 | 647381 | SRX21974759 | SRS19050622 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95345 | 0.95394 | 0.08901 | 0.08834 | 0.73537 | 0.73596 | 0.50012 | 0.49674 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28467 | 28467 | SRR26265242 | SRX21974758 | SRS19050621 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | IFN4 3 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 11|BioSampleModel:Model organism or animal | RNAseq of zebrafish | IFND3 | IFND3 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | IFN4-3.R1.fq.gz IFN4-3.R2.fq.gz | fastq fastq | 6983243474.0 | 23627912.0 | IFN4 3.R1.fq.gz | 0:147.80 1:147.75 | A:1880838380;C:1603492441;G:1611871993;T:1885974103;N:1066557 | 147 | 147 | 1880838380 | 1603492441 | 1611871993 | 1885974103 | 1066557 | SRX21974758 | SRS19050621 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95262 | 0.95399 | 0.09442 | 0.09269 | 0.73586 | 0.73519 | 0.50113 | 0.49912 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28468 | 28468 | SRR26265243 | SRX21974757 | SRS19050620 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | Control 2 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 2|BioSampleModel:Model organism or animal | RNAseq of zebrafish | C2 | C2 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | Control-2.R1.fq.gz Control-2.R2.fq.gz | fastq fastq | 7064416471.0 | 23901145.0 | Control 2.R1.fq.gz | 0:147.80 1:147.77 | A:1896430007;C:1626943513;G:1635235356;T:1905174563;N:633032 | 147 | 147 | 1896430007 | 1626943513 | 1635235356 | 1905174563 | 633032 | SRX21974757 | SRS19050620 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95546 | 0.95678 | 0.08984 | 0.08994 | 0.73535 | 0.73565 | 0.49891 | 0.49705 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 28469 | 28469 | SRR26265244 | SRX21974756 | SRS19050619 | SRP464312 | PRJNA1022576 | Danio rerio Raw sequence reads | PRJNA1022576 | Whole Genome Sequencing | In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis. | Control 1 | strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 1|BioSampleModel:Model organism or animal | RNAseq of zebrafish | C1 | C1 | normal RNA seq of zebrafish | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP464312 | Control-1.R1.fq.gz Control-1.R2.fq.gz | fastq fastq | 7005585889.0 | 23733330.0 | Control 1.R1.fq.gz | 0:147.61 1:147.57 | A:1874251473;C:1620035540;G:1628125464;T:1882607735;N:565677 | 147 | 147 | 1874251473 | 1620035540 | 1628125464 | 1882607735 | 565677 | SRX21974756 | SRS19050619 | SRA1725060 | Shanghai Ocean University|College of Fisheries and Life Science | Shanghai Ocean University | 2 | 0.95539 | 0.95612 | 0.08699 | 0.08663 | 0.73777 | 0.73833 | 0.49693 | 0.49816 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-10-03 | Undetermined | Undetermined | Cell Line | Cell Line | |||||||||||||||||||||
| 67836 | 67836 | SRR17386276 | SRX13560365 | SRS11453104 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | G7 3 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 9|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S131 | S131 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_7dpi3_Clean_Data1.fq.gz Gill_7dpi3_Clean_Data2.fq.gz | fastq fastq | 6714068679.0 | 23990941.0 | Gill 7dpi3 Clean Data1.fq.gz | 0:139.94 1:139.92 | A:1763959035;C:1585978862;G:1593569642;T:1770413859;N:147281 | 139 | 139 | 1763959035 | 1585978862 | 1593569642 | 1770413859 | 147281 | SRX13560365 | SRS11453104 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.9346 | 0.93604 | 0.05602 | 0.05525 | 0.69877 | 0.69761 | 0.5006 | 0.50091 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 67837 | 67837 | SRR17386277 | SRX13560364 | SRS11453103 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | G7 2 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 8|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S130 | S130 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_7dpi2_Clean_Data1.fq.gz Gill_7dpi2_Clean_Data2.fq.gz | fastq fastq | 6651799504.0 | 23755238.0 | Gill 7dpi2 Clean Data1.fq.gz | 0:140.01 1:140.00 | A:1739818732;C:1574969869;G:1589121073;T:1747742026;N:147804 | 140 | 140 | 1739818732 | 1574969869 | 1589121073 | 1747742026 | 147804 | SRX13560364 | SRS11453103 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.93216 | 0.93204 | 0.05441 | 0.05411 | 0.70021 | 0.70017 | 0.49971 | 0.50022 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 67838 | 67838 | SRR17386278 | SRX13560363 | SRS11453102 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | G7 1 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 7|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S129 | S129 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_7dpi1_Clean_Data1.fq.gz Gill_7dpi1_Clean_Data2.fq.gz | fastq fastq | 4992822830.0 | 17852500.0 | Gill 7dpi1 Clean Data1.fq.gz | 0:139.84 1:139.83 | A:1332570758;C:1157260526;G:1174499594;T:1328481612;N:10340 | 139 | 139 | 1332570758 | 1157260526 | 1174499594 | 1328481612 | 10340 | SRX13560363 | SRS11453102 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.9281 | 0.93065 | 0.06937 | 0.06833 | 0.69033 | 0.68893 | 0.50068 | 0.50026 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 67839 | 67839 | SRR17386279 | SRX13560362 | SRS11453101 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | G3 3 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 6|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S128 | S128 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_3dpi3_Clean_Data1.fq.gz Gill_3dpi3_Clean_Data2.fq.gz | fastq fastq | 6997831816.0 | 24954040.0 | Gill 3dpi3 Clean Data1.fq.gz | 0:140.22 1:140.21 | A:1830864881;C:1655547632;G:1672630082;T:1838637853;N:151368 | 140 | 140 | 1830864881 | 1655547632 | 1672630082 | 1838637853 | 151368 | SRX13560362 | SRS11453101 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.93226 | 0.93407 | 0.04804 | 0.04727 | 0.71981 | 0.71881 | 0.48198 | 0.48333 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 67840 | 67840 | SRR17386280 | SRX13560361 | SRS11453100 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | G3 2 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S127 | S127 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_3dpi2_Clean_Data1.fq.gz Gill_3dpi2_Clean_Data2.fq.gz | fastq fastq | 7042078942.0 | 25114470.0 | Gill 3dpi2 Clean Data1.fq.gz | 0:140.21 1:140.19 | A:1839895370;C:1667692247;G:1684937624;T:1849401074;N:152627 | 140 | 140 | 1839895370 | 1667692247 | 1684937624 | 1849401074 | 152627 | SRX13560361 | SRS11453100 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.93037 | 0.93106 | 0.04787 | 0.04704 | 0.71956 | 0.71833 | 0.4789 | 0.48397 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 67841 | 67841 | SRR17386281 | SRX13560360 | SRS11453099 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | G3 1 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 4|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S126 | S126 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_3dpi1_Clean_Data1.fq.gz Gill_3dpi1_Clean_Data2.fq.gz | fastq fastq | 6795179593.0 | 24546282.0 | Gill 3dpi1 Clean Data1.fq.gz | 0:138.41 1:138.42 | A:1740617128;C:1653484959;G:1667383107;T:1733667548;N:26851 | 138 | 138 | 1740617128 | 1653484959 | 1667383107 | 1733667548 | 26851 | SRX13560360 | SRS11453099 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.93975 | 0.93965 | 0.04328 | 0.04269 | 0.71908 | 0.72032 | 0.47917 | 0.47612 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 67842 | 67842 | SRR17386282 | SRX13560359 | SRS11453098 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | ck 3 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S125 | S125 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_con3_Clean_Data1.fq.gz Gill_con3_Clean_Data2.fq.gz | fastq fastq | 6532623508.0 | 23299642.0 | Gill con3 Clean Data1.fq.gz | 0:140.19 1:140.18 | A:1719338437;C:1532877064;G:1551680948;T:1728585867;N:141192 | 140 | 140 | 1719338437 | 1532877064 | 1551680948 | 1728585867 | 141192 | SRX13560359 | SRS11453098 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.93634 | 0.93701 | 0.0531 | 0.05253 | 0.72936 | 0.72977 | 0.48876 | 0.49167 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 67843 | 67843 | SRR17386283 | SRX13560358 | SRS11453097 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | ck 2 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S124 | S124 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_con2_Clean_Data1.fq.gz Gill_con2_Clean_Data2.fq.gz | fastq fastq | 5961805472.0 | 21275022.0 | Gill con2 Clean Data1.fq.gz | 0:140.12 1:140.11 | A:1562509100;C:1405898016;G:1423494829;T:1569772023;N:131504 | 140 | 140 | 1562509100 | 1405898016 | 1423494829 | 1569772023 | 131504 | SRX13560358 | SRS11453097 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.93445 | 0.93628 | 0.04993 | 0.04957 | 0.73182 | 0.73077 | 0.48248 | 0.49573 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 67844 | 67844 | SRR17386284 | SRX13560357 | SRS11453096 | SRP352979 | PRJNA793147 | Danio rerio Raw sequence reads | PRJNA793147 | Whole Genome Sequencing | normal RNA seq of Danio rerio | ck 1 | strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal | RNAseq of Danio rerio | S123 | S123 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP352979 | Gill_con1_Clean_Data1.fq.gz Gill_con1_Clean_Data2.fq.gz | fastq fastq | 5140938459.0 | 18343430.0 | Gill con1 Clean Data1.fq.gz | 0:140.14 1:140.12 | A:1372431897;C:1190016635;G:1209788123;T:1368690050;N:11754 | 140 | 140 | 1372431897 | 1190016635 | 1209788123 | 1368690050 | 11754 | SRX13560357 | SRS11453096 | SRA1350370 | Northwest A&F University|College of Animal Science and Technology | Northwest A&F University | 2 | 0.92642 | 0.93067 | 0.06487 | 0.06429 | 0.72529 | 0.72403 | 0.51099 | 0.51071 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-30 | Undetermined | Undetermined | Gill | Respiratory System | |||||||||||||||||||||
| 70225 | 70225 | SRR19627917 | SRX15678474 | SRS13376477 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 9 FAC hypoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:3 0.1% O2 with FAC supplementation|BioSampleModel:Model organism or animal | FAC hypoxia 3 | FAC hypoxia 3 | FAC hypoxia 3 | supplemrntation with FAC and hypoxia for 5d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | FAC_hypoxia-3.R1.fastq.gz FAC_hypoxia-3.R2.fastq.gz | fastq fastq | 6380199000.0 | 21267330.0 | FAC hypoxia 3.R1.fastq.gz | 0:150 1:150 | A:1671433136;C:1499373647;G:1576679120;T:1632651556;N:61541 | 150 | 150 | 1671433136 | 1499373647 | 1576679120 | 1632651556 | 61541 | SRX15678474 | SRS13376477 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.95363 | 0.95459 | 0.05881 | 0.05873 | 0.76631 | 0.76577 | 0.53835 | 0.52835 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70226 | 70226 | SRR19627918 | SRX15678473 | SRS13376476 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 8 FAC hypoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:2 0.1% O2 with FAC supplementation|BioSampleModel:Model organism or animal | FAC hypoxia 2 | FAC hypoxia 2 | FAC hypoxia 2 | supplemrntation with FAC and hypoxia for 4d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | FAC_hypoxia-2.R1.fastq.gz FAC_hypoxia-2.R2.fastq.gz | fastq fastq | 6101829600.0 | 20339432.0 | FAC hypoxia 2.R1.fastq.gz | 0:150 1:150 | A:1574893595;C:1454868394;G:1547239872;T:1524768201;N:59538 | 150 | 150 | 1574893595 | 1454868394 | 1547239872 | 1524768201 | 59538 | SRX15678473 | SRS13376476 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.95634 | 0.95739 | 0.05342 | 0.05362 | 0.76881 | 0.76749 | 0.53034 | 0.53011 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70227 | 70227 | SRR19627919 | SRX15678472 | SRS13376475 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 7 FAC hypoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:1 0.1% O2 with FAC supplementation|BioSampleModel:Model organism or animal | FAC hypoxia 1 | FAC hypoxia 1 | FAC hypoxia 1 | supplemrntation with FAC and hypoxia for 3d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | FAC_hypoxia-1.R1.fastq.gz FAC_hypoxia-1.R2.fastq.gz | fastq fastq | 6414187800.0 | 21380626.0 | FAC hypoxia 1.R1.fastq.gz | 0:150 1:150 | A:1641953069;C:1546854359;G:1629263103;T:1596055004;N:62265 | 150 | 150 | 1641953069 | 1546854359 | 1629263103 | 1596055004 | 62265 | SRX15678472 | SRS13376475 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.95903 | 0.9597 | 0.0736 | 0.0737 | 0.7723 | 0.77045 | 0.54827 | 0.55406 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70228 | 70228 | SRR19627920 | SRX15678471 | SRS13376474 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 6 WT hypoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:3 0.1% O2|BioSampleModel:Model organism or animal | WT hypoxia 3 | WT hypoxia 3 | WT hypoxia 3 | hypoxia for 3d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | WT_hypoxia-3.R1.fastq.gz WT_hypoxia-3.R2.fastq.gz | fastq fastq | 6841301400.0 | 22804338.0 | WT hypoxia 3.R1.fastq.gz | 0:150 1:150 | A:1750979097;C:1640750395;G:1756510566;T:1692995648;N:65694 | 150 | 150 | 1750979097 | 1640750395 | 1756510566 | 1692995648 | 65694 | SRX15678471 | SRS13376474 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.95521 | 0.95574 | 0.05844 | 0.05863 | 0.76889 | 0.76745 | 0.52412 | 0.5208 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70229 | 70229 | SRR19627921 | SRX15678470 | SRS13376473 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 5 WT hypoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:2 0.1% O2|BioSampleModel:Model organism or animal | WT hypoxia 2 | WT hypoxia 2 | WT hypoxia 2 | hypoxia for 3d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | WT_hypoxia-2.R1.fastq.gz WT_hypoxia-2.R2.fastq.gz | fastq fastq | 7296870000.0 | 24322900.0 | WT hypoxia 2.R1.fastq.gz | 0:150 1:150 | A:1872215969;C:1749380281;G:1856930287;T:1818277482;N:65981 | 150 | 150 | 1872215969 | 1749380281 | 1856930287 | 1818277482 | 65981 | SRX15678470 | SRS13376473 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.95541 | 0.95711 | 0.05508 | 0.05529 | 0.77528 | 0.77498 | 0.52698 | 0.52686 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70230 | 70230 | SRR19627922 | SRX15678469 | SRS13376472 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 4 WT hypoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:1 0.1% O2|BioSampleModel:Model organism or animal | WT hypoxia 1 | WT hypoxia 1 | WT hypoxia 1 | hypoxia for 3d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | WT_hypoxia-1.R1.fastq.gz WT_hypoxia-1.R2.fastq.gz | fastq fastq | 6122333700.0 | 20407779.0 | WT hypoxia 1.R1.fastq.gz | 0:150 1:150 | A:1596743120;C:1445830065;G:1529572290;T:1550128482;N:59743 | 150 | 150 | 1596743120 | 1445830065 | 1529572290 | 1550128482 | 59743 | SRX15678469 | SRS13376472 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.9487 | 0.94932 | 0.06381 | 0.0636 | 0.75883 | 0.75856 | 0.52097 | 0.52495 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70231 | 70231 | SRR19627923 | SRX15678468 | SRS13376471 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 3 WT normoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:3 21% O2|BioSampleModel:Model organism or animal | WT normoxia 3 | WT normoxia 3 | WT normoxia 3 | normoxia for 3d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | WT_normoxia-3.R1.fastq.gz WT_normoxia-3.R2.fastq.gz | fastq fastq | 6129969300.0 | 20433231.0 | WT normoxia 3.R1.fastq.gz | 0:150 1:150 | A:1603815001;C:1446155900;G:1518644535;T:1561242175;N:111689 | 150 | 150 | 1603815001 | 1446155900 | 1518644535 | 1561242175 | 111689 | SRX15678468 | SRS13376471 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.9511 | 0.94975 | 0.06489 | 0.06398 | 0.75653 | 0.75832 | 0.5219 | 0.51649 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70232 | 70232 | SRR19627924 | SRX15678467 | SRS13376470 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 2 WT normoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:2 21% O2|BioSampleModel:Model organism or animal | WT normoxia 2 | WT normoxia 2 | WT normoxia 2 | normoxia for 3d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | WT_normoxia-2.R1.fastq.gz WT_normoxia-2.R2.fastq.gz | fastq fastq | 6477041700.0 | 21590139.0 | WT normoxia 2.R1.fastq.gz | 0:150 1:150 | A:1689277340;C:1533072440;G:1600344997;T:1654227811;N:119112 | 150 | 150 | 1689277340 | 1533072440 | 1600344997 | 1654227811 | 119112 | SRX15678467 | SRS13376470 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.95025 | 0.9486 | 0.06318 | 0.06262 | 0.75816 | 0.75933 | 0.49794 | 0.50063 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70233 | 70233 | SRR19627925 | SRX15678466 | SRS13376469 | SRP379658 | PRJNA848069 | Transcriptome analysis of ZFL cells | PRJNA848069 | Other | the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress | 1 WT normoxia | isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:1 21% O2|BioSampleModel:Model organism or animal | WT normoxia 1 | WT normoxia 1 | WT normoxia 1 | normoxia for 3d | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379658 | WT_normoxia-1.R1.fastq.gz WT_normoxia-1.R2.fastq.gz | fastq fastq | 7612447200.0 | 25374824.0 | WT normoxia 1.R1.fastq.gz | 0:150 1:150 | A:1995483560;C:1776838669;G:1907898454;T:1932088660;N:137857 | 150 | 150 | 1995483560 | 1776838669 | 1907898454 | 1932088660 | 137857 | SRX15678466 | SRS13376469 | SRA1435736 | SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science | SHANGHAI OCEAN UNIVERSITY | 2 | 0.94638 | 0.94688 | 0.06242 | 0.06151 | 0.76506 | 0.76524 | 0.53233 | 0.53157 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-11 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70307 | 70307 | SRR19661767 | SRX15711495 | SRS13405890 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h3 S3 L004 R1 | strain:not collected|isolate:71|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 71 | 96h3 S3 L004 R1 | 96h3 S3 L004 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h3_S3_L004_R1_001.fastq.gz 96h3_S3_L004_R2_001.fastq.gz | fastq fastq | 724691152.0 | 3367984.0 | 96h3 S3 L004 R1 001.fastq.gz | 0:107.15 1:108.02 | A:197062569;C:164860065;G:168446417;T:193112518;N:1209583 | 107 | 108 | 197062569 | 164860065 | 168446417 | 193112518 | 1209583 | SRX15711495 | SRS13405890 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.74397 | 0.74651 | 0.05835 | 0.05714 | 0.92417 | 0.92638 | 0.5822 | 0.56964 | 151 | 151 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70308 | 70308 | SRR19661768 | SRX15711494 | SRS13405889 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h3 S3 L002 R1 | strain:not collected|isolate:67|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 67 | 96h3 S3 L002 R1 | 96h3 S3 L002 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h3_S3_L002_R1_001.fastq.gz 96h3_S3_L002_R2_001.fastq.gz | fastq fastq | 727527211.0 | 3371310.0 | 96h3 S3 L002 R1 001.fastq.gz | 0:107.54 1:108.26 | A:197175975;C:166079247;G:169466504;T:193755887;N:1049598 | 107 | 108 | 197175975 | 166079247 | 169466504 | 193755887 | 1049598 | SRX15711494 | SRS13405889 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.74895 | 0.75162 | 0.05798 | 0.05783 | 0.92437 | 0.92624 | 0.5779 | 0.58024 | 151 | 151 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70309 | 70309 | SRR19661769 | SRX15711493 | SRS13405888 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h3 S3 L003 R1 | strain:not collected|isolate:69|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 69 | 96h3 S3 L003 R1 | 96h3 S3 L003 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h3_S3_L003_R1_001.fastq.gz 96h3_S3_L003_R2_001.fastq.gz | fastq fastq | 721854182.0 | 3340952.0 | 96h3 S3 L003 R1 001.fastq.gz | 0:107.31 1:108.75 | A:195623831;C:164092903;G:169487065;T:191319168;N:1331215 | 107 | 108 | 195623831 | 164092903 | 169487065 | 191319168 | 1331215 | SRX15711493 | SRS13405888 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.74368 | 0.7473 | 0.05837 | 0.0561 | 0.92393 | 0.92656 | 0.57838 | 0.58231 | 85 | 151 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70310 | 70310 | SRR19661770 | SRX15711492 | SRS13405887 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h3 S3 L001 R1 | strain:not collected|isolate:65|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 65 | 96h3 S3 L001 R1 | 96h3 S3 L001 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h3_S3_L001_R1_001.fastq.gz 96h3_S3_L001_R2_001.fastq.gz | fastq fastq | 762242971.0 | 3532224.0 | 96h3 S3 L001 R1 001.fastq.gz | 0:107.48 1:108.31 | A:206617375;C:173787104;G:177521573;T:203129341;N:1187578 | 107 | 108 | 206617375 | 173787104 | 177521573 | 203129341 | 1187578 | SRX15711492 | SRS13405887 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.74834 | 0.75267 | 0.0597 | 0.05817 | 0.92303 | 0.92567 | 0.5831 | 0.57326 | 146 | 146 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70311 | 70311 | SRR19661771 | SRX15711491 | SRS13405886 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h2 S2 L004 R1 | strain:not collected|isolate:63|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 63 | 96h2 S2 L004 R1 | 96h2 S2 L004 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h2_S2_L004_R1_001.fastq.gz 96h2_S2_L004_R2_001.fastq.gz | fastq fastq | 845984162.0 | 3811397.0 | 96h2 S2 L004 R1 001.fastq.gz | 0:110.73 1:111.23 | A:236008235;C:187170277;G:189684416;T:231733347;N:1387887 | 110 | 111 | 236008235 | 187170277 | 189684416 | 231733347 | 1387887 | SRX15711491 | SRS13405886 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.66556 | 0.66544 | 0.09293 | 0.09318 | 0.93639 | 0.93714 | 0.72978 | 0.68324 | 114 | 114 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70312 | 70312 | SRR19661772 | SRX15711490 | SRS13405885 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h2 S2 L003 R1 | strain:not collected|isolate:61|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 61 | 96h2 S2 L003 R1 | 96h2 S2 L003 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h2_S2_L003_R1_001.fastq.gz 96h2_S2_L003_R2_001.fastq.gz | fastq fastq | 846762783.0 | 3804936.0 | 96h2 S2 L003 R1 001.fastq.gz | 0:110.86 1:111.68 | A:235667561;C:187507879;G:191010208;T:231046960;N:1530175 | 110 | 111 | 235667561 | 187507879 | 191010208 | 231046960 | 1530175 | SRX15711490 | SRS13405885 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.66396 | 0.66167 | 0.09179 | 0.09248 | 0.93681 | 0.93779 | 0.72854 | 0.72792 | 151 | 148 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70314 | 70314 | SRR19661774 | SRX15711488 | SRS13405883 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h2 S2 L002 R1 | strain:not collected|isolate:59|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 59 | 96h2 S2 L002 R1 | 96h2 S2 L002 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h2_S2_L002_R1_001.fastq.gz 96h2_S2_L002_R2_001.fastq.gz | fastq fastq | 845982861.0 | 3805872.0 | 96h2 S2 L002 R1 001.fastq.gz | 0:110.92 1:111.36 | A:235182018;C:187851706;G:190217754;T:231550269;N:1181114 | 110 | 111 | 235182018 | 187851706 | 190217754 | 231550269 | 1181114 | SRX15711488 | SRS13405883 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.66702 | 0.6654 | 0.09164 | 0.09209 | 0.93687 | 0.93708 | 0.72779 | 0.71408 | 88 | 88 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70315 | 70315 | SRR19661775 | SRX15711487 | SRS13405882 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h2 S2 L001 R1 | strain:not collected|isolate:57|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 57 | 96h2 S2 L001 R1 | 96h2 S2 L001 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h2_S2_L001_R1_001.fastq.gz 96h2_S2_L001_R2_001.fastq.gz | fastq fastq | 882891930.0 | 3974505.0 | 96h2 S2 L001 R1 001.fastq.gz | 0:110.84 1:111.29 | A:245671001;C:195781216;G:198293079;T:241773279;N:1373355 | 110 | 111 | 245671001 | 195781216 | 198293079 | 241773279 | 1373355 | SRX15711487 | SRS13405882 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.66784 | 0.6674 | 0.09175 | 0.09241 | 0.93649 | 0.93679 | 0.74072 | 0.73919 | 151 | 151 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70316 | 70316 | SRR19661776 | SRX15711486 | SRS13405881 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h1 S10 L004 R1 | strain:not collected|isolate:55|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 55 | 96h1 S10 L004 R1 | 96h1 S10 L004 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h1_S10_L004_R1_001.fastq.gz 96h1_S10_L004_R2_001.fastq.gz | fastq fastq | 1077112140.0 | 5018713.0 | 96h1 S10 L004 R1 001.fastq.gz | 0:107.02 1:107.60 | A:273194658;C:265896919;G:267463814;T:268517738;N:2039011 | 107 | 107 | 273194658 | 265896919 | 267463814 | 268517738 | 2039011 | SRX15711486 | SRS13405881 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.80791 | 0.8093 | 0.01606 | 0.01588 | 0.91539 | 0.91612 | 0.53854 | 0.54331 | 141 | 141 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70317 | 70317 | SRR19661777 | SRX15711485 | SRS13405880 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h1 S10 L003 R1 | strain:not collected|isolate:53|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 53 | 96h1 S10 L003 R1 | 96h1 S10 L003 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h1_S10_L003_R1_001.fastq.gz 96h1_S10_L003_R2_001.fastq.gz | fastq fastq | 1074756611.0 | 4991643.0 | 96h1 S10 L003 R1 001.fastq.gz | 0:107.24 1:108.07 | A:272103314;C:265302436;G:267889842;T:267221510;N:2239509 | 107 | 108 | 272103314 | 265302436 | 267889842 | 267221510 | 2239509 | SRX15711485 | SRS13405880 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.80776 | 0.80844 | 0.01589 | 0.01627 | 0.91549 | 0.91656 | 0.51447 | 0.54362 | 134 | 134 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70318 | 70318 | SRR19661778 | SRX15711484 | SRS13405878 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h1 S10 L002 R1 | strain:not collected|isolate:51|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 51 | 96h1 S10 L002 R1 | 96h1 S10 L002 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h1_S10_L002_R1_001.fastq.gz 96h1_S10_L002_R2_001.fastq.gz | fastq fastq | 1078450197.0 | 5011831.0 | 96h1 S10 L002 R1 001.fastq.gz | 0:107.34 1:107.84 | A:272752630;C:266870723;G:268309236;T:268749597;N:1768011 | 107 | 107 | 272752630 | 266870723 | 268309236 | 268749597 | 1768011 | SRX15711484 | SRS13405878 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.81048 | 0.81121 | 0.01619 | 0.01654 | 0.9153 | 0.91612 | 0.54078 | 0.51723 | 66 | 66 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 70320 | 70320 | SRR19661780 | SRX15711482 | SRS13405876 | SRP381845 | PRJNA849172 | Danio rerio Raw sequence reads | PRJNA849172 | Other | Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf. | 96h1 S10 L001 R1 | strain:not collected|isolate:49|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal | 49 | 96h1 S10 L001 R1 | 96h1 S10 L001 R1 | sorting | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP381845 | 96h1_S10_L001_R1_001.fastq.gz 96h1_S10_L001_R2_001.fastq.gz | fastq fastq | 1117312777.0 | 5199971.0 | 96h1 S10 L001 R1 001.fastq.gz | 0:107.20 1:107.67 | A:282784515;C:276288506;G:277648990;T:278602261;N:1988505 | 107 | 107 | 282784515 | 276288506 | 277648990 | 278602261 | 1988505 | SRX15711482 | SRS13405876 | SRA1437609 | Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat | Institute of Hydrobiology, Chinese Academy of Sciences | 2 | 0.8105 | 0.81088 | 0.01585 | 0.0163 | 0.91496 | 0.91555 | 0.49744 | 0.5474 | 73 | 73 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-06-15 | Undetermined | Undetermined | Liver | Liver and Biliary System | |||||||||||||||||||||
| 71972 | 71972 | SRR22163682 | SRX18142568 | SRS15644032 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | C3 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:control|replicate:replicate3|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | C3 | C3 | control group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | C3.R1.fastq.gz C3.R2.fastq.gz | fastq fastq | 6777299176.0 | 22441388.0 | C3.R1.fastq.gz | 0:151 1:151 | A:1869146927;C:1513142912;G:1565477798;T:1829395893;N:135646 | 151 | 151 | 1869146927 | 1513142912 | 1565477798 | 1829395893 | 135646 | SRX18142568 | SRS15644032 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.91581 | 0.91452 | 0.09416 | 0.09344 | 0.71167 | 0.71338 | 0.50247 | 0.50311 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 71973 | 71973 | SRR22163683 | SRX18142567 | SRS15644031 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | C2 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:control|replicate:replicate2|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | C2 | C2 | control group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | C2.R1.fastq.gz C2.R2.fastq.gz | fastq fastq | 6956425644.0 | 23034522.0 | C2.R1.fastq.gz | 0:151 1:151 | A:1847551873;C:1616308106;G:1662475314;T:1829952767;N:137584 | 151 | 151 | 1847551873 | 1616308106 | 1662475314 | 1829952767 | 137584 | SRX18142567 | SRS15644031 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.93033 | 0.9312 | 0.056 | 0.05619 | 0.71261 | 0.71376 | 0.4668 | 0.47014 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 71974 | 71974 | SRR22163684 | SRX18142566 | SRS15644030 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | C1 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:control|replicate:replicate1|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | C1 | C1 | control group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | C1.R1.fastq.gz C1.R2.fastq.gz | fastq fastq | 6218689172.0 | 20591686.0 | C1.R1.fastq.gz | 0:151 1:151 | A:1651743119;C:1444992966;G:1490934383;T:1630891482;N:127222 | 151 | 151 | 1651743119 | 1444992966 | 1490934383 | 1630891482 | 127222 | SRX18142566 | SRS15644030 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.93571 | 0.93627 | 0.03427 | 0.0346 | 0.73336 | 0.73401 | 0.47064 | 0.47601 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 71975 | 71975 | SRR22163685 | SRX18142565 | SRS15644029 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | B3 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:challenge|replicate:replicate3|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | B3 | B3 | challenge group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | B3.R1.fastq.gz B3.R2.fastq.gz | fastq fastq | 7958268062.0 | 26351881.0 | B3.R1.fastq.gz | 0:151 1:151 | A:2067039750;C:1894612680;G:1943559820;T:2052891379;N:164433 | 151 | 151 | 2067039750 | 1894612680 | 1943559820 | 2052891379 | 164433 | SRX18142565 | SRS15644029 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.93754 | 0.93809 | 0.03309 | 0.03347 | 0.71762 | 0.71731 | 0.49012 | 0.4888 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 71976 | 71976 | SRR22163686 | SRX18142564 | SRS15644028 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | B2 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:challenge|replicate:replicate2|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | B2 | B2 | challenge group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | B2.R1.fastq.gz B2.R2.fastq.gz | fastq fastq | 7071097158.0 | 23414229.0 | B2.R1.fastq.gz | 0:151 1:151 | A:1862299896;C:1658740196;G:1713471478;T:1836444697;N:140891 | 151 | 151 | 1862299896 | 1658740196 | 1713471478 | 1836444697 | 140891 | SRX18142564 | SRS15644028 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.94335 | 0.94369 | 0.04139 | 0.04172 | 0.80405 | 0.80415 | 0.39649 | 0.39674 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 71977 | 71977 | SRR22163687 | SRX18142563 | SRS15644027 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | B1 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:challenge|replicate:replicate1|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | B1 | B1 | challenge group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | B1.R1.fastq.gz B1.R2.fastq.gz | fastq fastq | 7597788178.0 | 25158239.0 | B1.R1.fastq.gz | 0:151 1:151 | A:1986638730;C:1797302173;G:1839273564;T:1974418679;N:155032 | 151 | 151 | 1986638730 | 1797302173 | 1839273564 | 1974418679 | 155032 | SRX18142563 | SRS15644027 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.93891 | 0.93921 | 0.04922 | 0.04888 | 0.74552 | 0.74501 | 0.48725 | 0.49058 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 71978 | 71978 | SRR22163688 | SRX18142562 | SRS15644026 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | A3 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:treatment|replicate:replicate3|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | A3 | A3 | treatment group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | A3.R1.fastq.gz A3.R2.fastq.gz | fastq fastq | 8674550152.0 | 28723676.0 | A3.R1.fastq.gz | 0:151 1:151 | A:2234032232;C:2083164440;G:2128058461;T:2229111717;N:183302 | 151 | 151 | 2234032232 | 2083164440 | 2128058461 | 2229111717 | 183302 | SRX18142562 | SRS15644026 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.93839 | 0.93828 | 0.01889 | 0.01887 | 0.73639 | 0.73724 | 0.48841 | 0.47397 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 71979 | 71979 | SRR22163689 | SRX18142561 | SRS15644025 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | A2 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:treatment|replicate:replicate2|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | A2 | A2 | treatment group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | A2.R1.fastq.gz A2.R2.fastq.gz | fastq fastq | 7383660816.0 | 24449208.0 | A2.R1.fastq.gz | 0:151 1:151 | A:1917884453;C:1759507724;G:1796259178;T:1909857526;N:151935 | 151 | 151 | 1917884453 | 1759507724 | 1796259178 | 1909857526 | 151935 | SRX18142561 | SRS15644025 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.93853 | 0.93854 | 0.02662 | 0.02663 | 0.71435 | 0.7149 | 0.49509 | 0.49212 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 71980 | 71980 | SRR22163690 | SRX18142560 | SRS15644024 | SRP405990 | PRJNA897077 | Transcriptome of zebrafish Danio rerio | PRJNA897077 | Other | Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing. | A1 | strain:not applicable|age:not collected|sex:not collected|tissue:spleen|treatment:treatment|replicate:replicate1|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | A1 | A1 | treatment group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP405990 | A1.R1.fastq.gz A1.R2.fastq.gz | fastq fastq | 7734454352.0 | 25610776.0 | A1.R1.fastq.gz | 0:151 1:151 | A:2031967267;C:1817027018;G:1866115793;T:2019187811;N:156463 | 151 | 151 | 2031967267 | 1817027018 | 1866115793 | 2019187811 | 156463 | SRX18142560 | SRS15644024 | SRA1532870 | Kunming University of Science and Technology|Faculty of Life Science and Technology | Kunming University of Science and Technology | 2 | 0.93755 | 0.93728 | 0.03692 | 0.03688 | 0.71664 | 0.71693 | 0.48577 | 0.48719 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2022-11-02 | Undetermined | Undetermined | Spleen | Hematopoietic System | |||||||||||||||||||||
| 74351 | 74351 | SRR23683737 | SRX19546501 | SRS16931906 | SRP425270 | PRJNA940319 | Danio rerio Raw sequence reads | PRJNA940319 | Whole Genome Sequencing | normal RNA seq of Danio rerio | WT 3 | WT3 3 LEG6615 | strain:not determined|isolate:not determined|breed:yes|cultivar:no|ecotype:not determined|age:not determined|dev stage:not determined|sex:not determined|tissue:brain|sample type:RNA seq|replicate:replicate=biological replicate 6|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | S1334 | S1334 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP425270 | WT3-3-LEG6615_L1_1.fq.gz WT3-3-LEG6615_L1_2.fq.gz | fastq fastq | 6010930500.0 | 20036435.0 | WT3 3 LEG6615 L1 1.fq.gz | 0:150 1:150 | A:1652361392;C:1354680737;G:1428533735;T:1575302026;N:52610 | 150 | 150 | 1652361392 | 1354680737 | 1428533735 | 1575302026 | 52610 | SRX19546501 | SRS16931906 | SRA1598033 | WuYi University|School of Biotechnology and Health Sciences | WuYi University | 2 | 0.93099 | 0.93249 | 0.04478 | 0.0449 | 0.74874 | 0.75079 | 0.46658 | 0.46534 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-03-02 | Undetermined | Undetermined | Brain | Nervous System | ||||||||||||||||||||
| 74352 | 74352 | SRR23683738 | SRX19546500 | SRS16931905 | SRP425270 | PRJNA940319 | Danio rerio Raw sequence reads | PRJNA940319 | Whole Genome Sequencing | normal RNA seq of Danio rerio | WT 2 | WT3 1 LEG6613 | strain:not determined|isolate:not determined|breed:yes|cultivar:no|ecotype:not determined|age:not determined|dev stage:not determined|sex:not determined|tissue:brain|sample type:RNA seq|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | S1333 | S1333 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP425270 | WT3-1-LEG6613_L1_1.fq.gz WT3-1-LEG6613_L1_2.fq.gz | fastq fastq | 5822410800.0 | 19408036.0 | WT3 1 LEG6613 L1 1.fq.gz | 0:150 1:150 | A:1773220549;C:1139612382;G:1197816098;T:1711712045;N:49726 | 150 | 150 | 1773220549 | 1139612382 | 1197816098 | 1711712045 | 49726 | SRX19546500 | SRS16931905 | SRA1598033 | WuYi University|School of Biotechnology and Health Sciences | WuYi University | 2 | 0.92172 | 0.92168 | 0.19562 | 0.19529 | 0.74014 | 0.74261 | 0.57512 | 0.57778 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-03-02 | Undetermined | Undetermined | Brain | Nervous System | ||||||||||||||||||||
| 74353 | 74353 | SRR23683739 | SRX19546499 | SRS16931904 | SRP425270 | PRJNA940319 | Danio rerio Raw sequence reads | PRJNA940319 | Whole Genome Sequencing | normal RNA seq of Danio rerio | WT 1 | WT2 3 LEG6611 | strain:not determined|isolate:not determined|breed:yes|cultivar:no|ecotype:not determined|age:not determined|dev stage:not determined|sex:not determined|tissue:brain|sample type:RNA seq|replicate:replicate=biological replicate 4|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | S1332 | S1332 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP425270 | WT2-3-LEG6611_L1_1.fq.gz WT2-3-LEG6611_L1_2.fq.gz | fastq fastq | 5805684900.0 | 19352283.0 | WT2 3 LEG6611 L1 1.fq.gz | 0:150 1:150 | A:1625581880;C:1276625062;G:1349838457;T:1553588972;N:50529 | 150 | 150 | 1625581880 | 1276625062 | 1349838457 | 1553588972 | 50529 | SRX19546499 | SRS16931904 | SRA1598033 | WuYi University|School of Biotechnology and Health Sciences | WuYi University | 2 | 0.85148 | 0.85202 | 0.0398 | 0.03963 | 0.76577 | 0.76684 | 0.49927 | 0.49769 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-03-02 | Undetermined | Undetermined | Brain | Nervous System | ||||||||||||||||||||
| 74354 | 74354 | SRR23683740 | SRX19546498 | SRS16931903 | SRP425270 | PRJNA940319 | Danio rerio Raw sequence reads | PRJNA940319 | Whole Genome Sequencing | normal RNA seq of Danio rerio | F0 3 | F02 3 LEG6590 | strain:not determined|isolate:not determined|breed:yes|cultivar:yes|ecotype:not determined|age:not determined|dev stage:not determined|sex:not determined|tissue:brain|sample type:RNA seq|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | S1331 | S1331 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP425270 | F02-3-LEG6590_L1_1.fq.gz F02-3-LEG6590_L1_2.fq.gz | fastq fastq | 6668811000.0 | 22229370.0 | F02 3 LEG6590 L1 1.fq.gz | 0:150 1:150 | A:1865250467;C:1462302193;G:1556060506;T:1785138343;N:59491 | 150 | 150 | 1865250467 | 1462302193 | 1556060506 | 1785138343 | 59491 | SRX19546498 | SRS16931903 | SRA1598033 | WuYi University|School of Biotechnology and Health Sciences | WuYi University | 2 | 0.93451 | 0.93559 | 0.05471 | 0.05424 | 0.82321 | 0.8258 | 0.52633 | 0.50978 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-03-02 | Undetermined | Undetermined | Brain | Nervous System | ||||||||||||||||||||
| 74355 | 74355 | SRR23683741 | SRX19546497 | SRS16931902 | SRP425270 | PRJNA940319 | Danio rerio Raw sequence reads | PRJNA940319 | Whole Genome Sequencing | normal RNA seq of Danio rerio | F0 2 | F02 1 LEG6588 | strain:not determined|isolate:not determined|breed:yes|cultivar:yes|ecotype:not determined|age:not determined|dev stage:not determined|sex:not determined|tissue:brain|sample type:RNA seq|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | S1330 | S1330 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP425270 | F02-1-LEG6588_L1_1.fq.gz F02-1-LEG6588_L1_2.fq.gz | fastq fastq | 6160540500.0 | 20535135.0 | F02 1 LEG6588 L1 1.fq.gz | 0:150 1:150 | A:1874432331;C:1208466682;G:1258708655;T:1818877772;N:55060 | 150 | 150 | 1874432331 | 1208466682 | 1258708655 | 1818877772 | 55060 | SRX19546497 | SRS16931902 | SRA1598033 | WuYi University|School of Biotechnology and Health Sciences | WuYi University | 2 | 0.91106 | 0.91132 | 0.18839 | 0.18725 | 0.73296 | 0.73547 | 0.55802 | 0.55925 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-03-02 | Undetermined | Undetermined | Brain | Nervous System | ||||||||||||||||||||
| 74356 | 74356 | SRR23683742 | SRX19546496 | SRS16931901 | SRP425270 | PRJNA940319 | Danio rerio Raw sequence reads | PRJNA940319 | Whole Genome Sequencing | normal RNA seq of Danio rerio | F0 1 | F01 3 LEG6586 | strain:not determined|isolate:not determined|breed:yes|cultivar:yes|ecotype:not determined|age:not determined|dev stage:not determined|sex:not determined|tissue:brain|sample type:RNA seq|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | S1329 | S1329 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP425270 | F01-3-LEG6586_L1_1.fq.gz F01-3-LEG6586_L1_2.fq.gz | fastq fastq | 7323739500.0 | 24412465.0 | F01 3 LEG6586 L1 1.fq.gz | 0:150 1:150 | A:2068711452;C:1588911003;G:1688920710;T:1977132262;N:64073 | 150 | 150 | 2068711452 | 1588911003 | 1688920710 | 1977132262 | 64073 | SRX19546496 | SRS16931901 | SRA1598033 | WuYi University|School of Biotechnology and Health Sciences | WuYi University | 2 | 0.93877 | 0.94114 | 0.04355 | 0.04273 | 0.80166 | 0.80302 | 0.6137 | 0.61898 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-03-02 | Undetermined | Undetermined | Brain | Nervous System | ||||||||||||||||||||
| 75099 | 75099 | SRR24295703 | SRX20091106 | SRS17422802 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S3 S0hpt S26 L003 R1 001.fastq | strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 9|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 0 hpt | 20201026 S3 S0hpt S26 L003 R1 001 | 20201026 S3 S0hpt S26 L003 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 30 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S3_S0hpt_S26_L003_R1_001.fastq.gz 20201026_S3_S0hpt_S26_L003_R2_001.fastq.gz | fastq fastq | 9523579187.0 | 53204353.0 | 20201026 S3 S0hpt S26 L003 R1 001.fastq.gz | 0:28 1:151 | A:2683643441;C:2130409626;G:2213828474;T:2495632325;N:65321 | 28 | 151 | 2683643441 | 2130409626 | 2213828474 | 2495632325 | 65321 | SRX20091106 | SRS17422802 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00736 | 0.92902 | 0.00193 | 0.10378 | 0.98815 | 0.81525 | 0.45394 | 0.60873 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75100 | 75100 | SRR24295704 | SRX20091105 | SRS17422801 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S3 S0hpt S8 L004 R1 001.fastq | strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 7|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 0 hpt | 20201026 S3 S0hpt S8 L004 R1 001 | 20201026 S3 S0hpt S8 L004 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 28 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S3_S0hpt_S8_L004_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L004_R2_001.fastq.gz | fastq fastq | 11268103342.0 | 62950298.0 | 20201026 S3 S0hpt S8 L004 R1 001.fastq.gz | 0:28 1:151 | A:3165223318;C:2522144425;G:2624994106;T:2955567304;N:174189 | 28 | 151 | 3165223318 | 2522144425 | 2624994106 | 2955567304 | 174189 | SRX20091105 | SRS17422801 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00779 | 0.92717 | 0.00206 | 0.1034 | 0.98776 | 0.81544 | 0.48375 | 0.57614 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75101 | 75101 | SRR24295705 | SRX20091104 | SRS17422800 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S3 S0hpt S8 L003 R1 001.fastq | strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 5|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 0 hpt | 20201026 S3 S0hpt S8 L003 R1 001 | 20201026 S3 S0hpt S8 L003 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 26 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S3_S0hpt_S8_L003_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L003_R2_001.fastq.gz | fastq fastq | 11318791667.0 | 63233473.0 | 20201026 S3 S0hpt S8 L003 R1 001.fastq.gz | 0:28 1:151 | A:3185910303;C:2527965947;G:2631985020;T:2972741298;N:189099 | 28 | 151 | 3185910303 | 2527965947 | 2631985020 | 2972741298 | 189099 | SRX20091104 | SRS17422800 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00736 | 0.92879 | 0.00199 | 0.10456 | 0.98827 | 0.81643 | 0.49224 | 0.57699 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75102 | 75102 | SRR24295706 | SRX20091103 | SRS17422798 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S3 S0hpt S8 L002 R1 001.fastq | strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 3|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 0 hpt | 20201026 S3 S0hpt S8 L002 R1 001 | 20201026 S3 S0hpt S8 L002 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 24 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S3_S0hpt_S8_L002_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L002_R2_001.fastq.gz | fastq fastq | 11212565191.0 | 62640029.0 | 20201026 S3 S0hpt S8 L002 R1 001.fastq.gz | 0:28 1:151 | A:3151088961;C:2508604162;G:2610615892;T:2942050613;N:205563 | 28 | 151 | 3151088961 | 2508604162 | 2610615892 | 2942050613 | 205563 | SRX20091103 | SRS17422798 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00781 | 0.92808 | 0.00205 | 0.10455 | 0.98744 | 0.81489 | 0.50675 | 0.61614 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75103 | 75103 | SRR24295707 | SRX20091102 | SRS17422799 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S3 S0hpt S8 L001 R1 001.fastq | strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 1|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 0 hpt | 20201026 S3 S0hpt S8 L001 R1 001 | 20201026 S3 S0hpt S8 L001 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 22 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S3_S0hpt_S8_L001_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L001_R2_001.fastq.gz | fastq fastq | 11551003355.0 | 64530745.0 | 20201026 S3 S0hpt S8 L001 R1 001.fastq.gz | 0:28 1:151 | A:3248866155;C:2582279236;G:2687784274;T:3031856357;N:217333 | 28 | 151 | 3248866155 | 2582279236 | 2687784274 | 3031856357 | 217333 | SRX20091102 | SRS17422799 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00773 | 0.92693 | 0.00213 | 0.10378 | 0.98796 | 0.81458 | 0.48003 | 0.61476 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75107 | 75107 | SRR24295711 | SRX20091098 | SRS17422794 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S2 S48hpt S25 L003 R1 001.fastq | strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 9|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 48 hpt | 20201026 S2 S48hpt S25 L003 R1 001 | 20201026 S2 S48hpt S25 L003 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 40 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S2_S48hpt_S25_L003_R1_001.fastq.gz 20201026_S2_S48hpt_S25_L003_R2_001.fastq.gz | fastq fastq | 14964717009.0 | 83601771.0 | 20201026 S2 S48hpt S25 L003 R1 001.fastq.gz | 0:28 1:151 | A:4042811725;C:3465477701;G:3602852950;T:3853470560;N:104073 | 28 | 151 | 4042811725 | 3465477701 | 3602852950 | 3853470560 | 104073 | SRX20091098 | SRS17422794 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00811 | 0.9409 | 0.00196 | 0.08687 | 0.98922 | 0.85001 | 0.51973 | 0.65526 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75108 | 75108 | SRR24295712 | SRX20091097 | SRS17422793 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S2 S48hpt S7 L004 R1 001.fastq | strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 7|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 48 hpt | 20201026 S2 S48hpt S7 L004 R1 001 | 20201026 S2 S48hpt S7 L004 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 38 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S2_S48hpt_S7_L004_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L004_R2_001.fastq.gz | fastq fastq | 10669333843.0 | 59605217.0 | 20201026 S2 S48hpt S7 L004 R1 001.fastq.gz | 0:28 1:151 | A:2876329901;C:2471017739;G:2573143323;T:2748679474;N:163406 | 28 | 151 | 2876329901 | 2471017739 | 2573143323 | 2748679474 | 163406 | SRX20091097 | SRS17422793 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00841 | 0.93868 | 0.00188 | 0.08847 | 0.98879 | 0.85149 | 0.54358 | 0.6538 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75109 | 75109 | SRR24295713 | SRX20091096 | SRS17422791 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S2 S48hpt S7 L003 R1 001.fastq | strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 5|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 48 hpt | 20201026 S2 S48hpt S7 L003 R1 001 | 20201026 S2 S48hpt S7 L003 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 36 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S2_S48hpt_S7_L003_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L003_R2_001.fastq.gz | fastq fastq | 10613956434.0 | 59295846.0 | 20201026 S2 S48hpt S7 L003 R1 001.fastq.gz | 0:28 1:151 | A:2867387827;C:2453215650;G:2555390367;T:2737785596;N:176994 | 28 | 151 | 2867387827 | 2453215650 | 2555390367 | 2737785596 | 176994 | SRX20091096 | SRS17422791 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00804 | 0.93909 | 0.00204 | 0.09014 | 0.98912 | 0.85289 | 0.53052 | 0.65123 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75110 | 75110 | SRR24295714 | SRX20091095 | SRS17422792 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S2 S48hpt S7 L002 R1 001.fastq | strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 3|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 48 hpt | 20201026 S2 S48hpt S7 L002 R1 001 | 20201026 S2 S48hpt S7 L002 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 34 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S2_S48hpt_S7_L002_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L002_R2_001.fastq.gz | fastq fastq | 10590029325.0 | 59162175.0 | 20201026 S2 S48hpt S7 L002 R1 001.fastq.gz | 0:28 1:151 | A:2855935581;C:2451968029;G:2552761582;T:2729169108;N:195025 | 28 | 151 | 2855935581 | 2451968029 | 2552761582 | 2729169108 | 195025 | SRX20091095 | SRS17422792 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00831 | 0.93901 | 0.00202 | 0.0879 | 0.98942 | 0.85072 | 0.5438 | 0.66125 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive System | |||||||||||||||||||||
| 75111 | 75111 | SRR24295715 | SRX20091094 | SRS17422790 | SRP434294 | PRJNA961336 | Single cell transcriptome sequence of intestinal regeneration in zebrafish | PRJNA961336 | Other | The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation. | 20201026 S2 S48hpt S7 L001 R1 001.fastq | strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 1|BioSampleModel:Model organism or animal | scRNA seq of zebrafish intestine: MTZ 48 hpt | 20201026 S2 S48hpt S7 L001 R1 001 | 20201026 S2 S48hpt S7 L001 R1 001 | Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 32 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP434294 | 20201026_S2_S48hpt_S7_L001_R2_001.fastq.gz 20201026_S2_S48hpt_S7_L001_R1_001.fastq.gz | fastq fastq | 10843243262.0 | 60576778.0 | 20201026 S2 S48hpt S7 L001 R1 001.fastq.gz | 0:28 1:151 | A:2926797989;C:2508866130;G:2611743790;T:2795632661;N:202692 | 28 | 151 | 2926797989 | 2508866130 | 2611743790 | 2795632661 | 202692 | SRX20091094 | SRS17422790 | SRA1626787 | Southwest University|Institute of Developmental Biology and Regenerativ | Southwest University | 2 | 0.00842 | 0.93796 | 0.00207 | 0.08873 | 0.98906 | 0.85204 | 0.53927 | 0.66266 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | China | 2023-04-25 | Undetermined | Undetermined | Gut | Digestive 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");;