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
8066,ERR035548,ERX013538,ERS017859,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult swim bladder,SAMEA782574,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782574|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult swim bladder|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:swim bladder|sample name:E MTAB 460:Zebrafish adult swim bladder|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460 part2:5625 5,ZFswimbladder 2 RNA 1523495,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented LiCl precipitated reverse transcribed with random primers a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.,Experimental Factor: ORGANISM PART:swim bladder,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,1600Application ReadForward11Technical ReadReverse772Application ReadReverse85,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16,5625_5.srf,srf,3631039360.0,22693996.0,E MTAB 460 part2:5625 5.srf,0:76 1:8 2:76,A:960241692;C:761151402;G:762172309;T:959064724;N:6857265,76,8,76,,960241692,761151402,762172309,959064724,6857265,ERX013538,ERS017859,ERA033503,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.86993,0.86373,0.16918,0.16735,0.68913,0.69384,0.50826,0.50673,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Swim Bladder,Swim Bladder
8068,ERR023148,ERX009450,ERS017859,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult swim bladder,SAMEA782574,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782574|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult swim bladder|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:swim bladder|sample name:E MTAB 460:Zebrafish adult swim bladder|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460:4191 5,RNA from Zebrafish adult swim bladder,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Experimental Factor: ORGANISM PART:swim bladder,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,1520Application ReadForward11Application ReadReverse77,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16,4191_5.srf,srf,4279981344.0,28157772.0,E MTAB 460:4191 5.srf,0:76 1:76,A:1465434155;C:660965580;G:667941564;T:1472658155;N:12981890,76,76,,,1465434155,660965580,667941564,1472658155,12981890,ERX009450,ERS017859,ERA015648,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.83269,0.83071,0.36856,0.36801,0.79746,0.79677,0.49125,0.4911,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Swim Bladder,Swim Bladder
8074,ERR023143,ERX009444,ERS017859,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult swim bladder,SAMEA782574,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782574|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult swim bladder|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:swim bladder|sample name:E MTAB 460:Zebrafish adult swim bladder|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460:3212 5,RNA from Zebrafish adult swim bladder,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Experimental Factor: ORGANISM PART:swim bladder,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,1520Application ReadForward11Application ReadReverse77,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16,3212_5.srf,srf,972304632.0,6396741.0,E MTAB 460:3212 5.srf,0:76 1:76,A:320388277;C:158735178;G:157312801;T:326747311;N:9121065,76,76,,,320388277,158735178,157312801,326747311,9121065,ERX009444,ERS017859,ERA015648,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.84363,0.84242,0.3398,0.33885,0.79082,0.78987,0.48696,0.50187,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Swim Bladder,Swim Bladder
28513,SRR31643557,SRX27006657,SRS23471106,SRP467901,PRJNA1026724,vertebrate lungs,PRJNA1026724,Other,We provide comprehensive datasets including RNA Seq and single cell RNA sequencing scRAN seq of multiple tissues for white spotted bamboo shark scRNA seq of multiple tissues of the African lungfish and Senegal bichir genome of the bearded dragon scRAN seq of African bullfrog lung and central bearded dragon lung and H3k27ac and H3k4me1 CUT&Tag sequencing data of chicken embryonic lungs from stage E9 to study the origin and evelution of vertebrate lungs.,,pubmed:39953253,,,zebrafish,,strain:Cyprinidae|age:adult|collection date:2021 09|geo loc name:China: Wuhan city Wuhan Province|sex:not collected|tissue:swim bladder|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish :swim blader,zebrafish swimbladder,zebrafish swimbladder,sequencing for single cell gene expression,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467901,,,Dr_Sb-3_S1_L003_R2_001.fastq.gz Dr_Sb-3_S1_L003_R1_001.fastq.gz Dr_Sb-2_S1_L001_R2_001.fastq.gz Dr_Sb-2_S1_L001_R1_001.fastq.gz Dr_Sb-1_S1_L001_R2_001.fastq.gz Dr_Sb-1_S1_L001_R1_001.fastq.gz,fastq fastq fastq fastq fastq fastq,,,Dr Sb 1 S1 L001 R1 001.fastq.gz,,,,,,,,,,,,SRX27006657,,SRA2029673,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2024-12-08,Adult,Adult,Swim Bladder,Swim Bladder
52152,SRR18181454,SRX14328418,SRS12144049,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Swim Bladder3,GSM5924292,,source name:swim bladder|strain:Tubingen|tissue:swim bladder|genotype:wild type,Swim Bladder3,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.,swim bladder,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:swim bladder|genotype:wild type,GSM5924292,GSM5924292: Swim Bladder3; Danio rerio; RNA Seq,GSM5924292,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924292,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,SwimBladder3.bam,bam,45191935800.0,150639786.0,GSM5924292 r1,0:150 1:150,A:10476251757;C:8049557401;G:8173647398;T:18490392981;N:2086263,150,150,,,10476251757,8049557401,8173647398,18490392981,2086263,SRX14328418,SRS12144049,SRA880843,GEO,Zhejiang University,2,0.0,0.76544,0.0,0.02769,1.0,0.86291,,0.51073,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Swim Bladder,Swim Bladder
52153,SRR18181453,SRX14328417,SRS12144048,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Swim Bladder2,GSM5924291,,source name:swim bladder|strain:Tubingen|tissue:swim bladder|genotype:wild type,Swim Bladder2,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.,swim bladder,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:swim bladder|genotype:wild type,GSM5924291,GSM5924291: Swim Bladder2; Danio rerio; RNA Seq,GSM5924291,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924291,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,SwimBladder2.bam,bam,18824466944.0,62332672.0,GSM5924291 r1,0:151 1:151,A:4604254176;C:3130145977;G:3233969707;T:7851792248;N:4304836,151,151,,,4604254176,3130145977,3233969707,7851792248,4304836,SRX14328417,SRS12144048,SRA880843,GEO,Zhejiang University,2,0.0,0.75695,0.0,0.03113,1.0,0.84346,,0.54953,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Swim Bladder,Swim Bladder
52199,SRR8991407,SRX5770475,SRS4704584,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Swim Bladder1,GSM3740960,,source name:swim bladder|strain:Tubingen|genotype:wild type|tissue:swim bladder,Swim Bladder1,The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.,swim bladder,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:swim bladder,GSM3740960,GSM3740960: SwimmingBladder1; Danio rerio; RNA Seq,GSM3740960,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740960,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,SwimmingBladder1.bam,bam,35046550662.0,116048181.0,GSM3740960 r1,0:151 1:151,A:8395527831;C:6153137560;G:6277460016;T:14213583474;N:6841781,151,151,,,8395527831,6153137560,6277460016,14213583474,6841781,SRX5770475,SRS4704584,SRA880843,GEO,Zhejiang University,2,0.0,0.82455,0.0,0.03727,1.0,0.85423,,0.53813,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Swim Bladder,Swim Bladder
55997,SRR10895904,SRX7564575,SRS6001799,SRP241982,PRJNA599026,Project of basal ray finned fishes,PRJNA599026,Other,The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.,,pubmed:33545088;pubmed:12470943,,,Zebrafish 004,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : adult,CL100103858 L02 9,CL100103858 L02 9,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,BGISEQ,BGISEQ-500,,SRP241982,,,CL100103858_L02_527_2.fq.gz CL100103858_L02_527_1.fq.gz,fastq fastq,9389292400.0,93892924.0,CL100103858 L02 527 1.fq.gz,0:100 1:100,A:2535177343;C:2107498353;G:2159172216;T:2574271698;N:13172790,100,100,,,2535177343,2107498353,2159172216,2574271698,13172790,SRX7564575,SRS6001799,SRA1026516,BGI|BGI-Research,BGI,1,0.94054,,0.10829,,0.70818,,0.51214,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-15,Adult,Adult,Swim Bladder,Swim Bladder
55998,SRR10895905,SRX7564574,SRS6001799,SRP241982,PRJNA599026,Project of basal ray finned fishes,PRJNA599026,Other,The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.,,pubmed:33545088;pubmed:12470943,,,Zebrafish 004,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : adult,CL100103178 L02 9,CL100103178 L02 9,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,BGISEQ,BGISEQ-500,,SRP241982,,,CL100103178_L02_580_2.fq.gz CL100103178_L02_580_1.fq.gz,fastq fastq,9451878800.0,94518788.0,CL100103178 L02 580 1.fq.gz,0:100 1:100,A:2482432185;C:2200816673;G:2254475373;T:2504225593;N:9928976,100,100,,,2482432185,2200816673,2254475373,2504225593,9928976,SRX7564574,SRS6001799,SRA1026516,BGI|BGI-Research,BGI,1,0.91363,,0.08854,,0.67399,,0.52315,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-15,Adult,Adult,Swim Bladder,Swim Bladder
55999,SRR10895906,SRX7564573,SRS6001799,SRP241982,PRJNA599026,Project of basal ray finned fishes,PRJNA599026,Other,The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.,,pubmed:33545088;pubmed:12470943,,,Zebrafish 004,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : adult,CL100103178 L02 8,CL100103178 L02 8,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,BGISEQ,BGISEQ-500,,SRP241982,,,CL100103178_L02_579_1.fq.gz CL100103178_L02_579_2.fq.gz,fastq fastq,6784370200.0,67843702.0,CL100103178 L02 579 1.fq.gz,0:100 1:100,A:1799307225;C:1565118646;G:1599826091;T:1813320759;N:6797479,100,100,,,1799307225,1565118646,1599826091,1813320759,6797479,SRX7564573,SRS6001799,SRA1026516,BGI|BGI-Research,BGI,1,0.91866,,0.10227,,0.71928,,0.50827,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-15,Adult,Adult,Swim Bladder,Swim Bladder
56000,SRR10895907,SRX7564572,SRS6001799,SRP241982,PRJNA599026,Project of basal ray finned fishes,PRJNA599026,Other,The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.,,pubmed:33545088;pubmed:12470943,,,Zebrafish 004,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : adult,CL100103858 L02 8,CL100103858 L02 8,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,BGISEQ,BGISEQ-500,,SRP241982,,,CL100103858_L02_529_2.fq.gz CL100103858_L02_529_1.fq.gz,fastq fastq,10614517200.0,106145172.0,CL100103858 L02 529 1.fq.gz,0:100 1:100,A:2821297968;C:2430515408;G:2486443963;T:2861653662;N:14606199,100,100,,,2821297968,2430515408,2486443963,2861653662,14606199,SRX7564572,SRS6001799,SRA1026516,BGI|BGI-Research,BGI,1,0.94747,,0.08863,,0.64632,,0.50637,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-15,Adult,Adult,Swim Bladder,Swim Bladder
56001,SRR10895908,SRX7564571,SRS6001799,SRP241982,PRJNA599026,Project of basal ray finned fishes,PRJNA599026,Other,The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.,,pubmed:33545088;pubmed:12470943,,,Zebrafish 004,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Swim bladder|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : adult,CL100103858 L02 7,CL100103858 L02 7,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,BGISEQ,BGISEQ-500,,SRP241982,,,CL100103858_L02_526_2.fq.gz CL100103858_L02_526_1.fq.gz,fastq fastq,8829000400.0,88290004.0,CL100103858 L02 526 1.fq.gz,0:100 1:100,A:2346419057;C:2025176439;G:2073455037;T:2371666164;N:12283703,100,100,,,2346419057,2025176439,2073455037,2371666164,12283703,SRX7564571,SRS6001799,SRA1026516,BGI|BGI-Research,BGI,1,0.93744,,0.08552,,0.70918,,0.49156,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-15,Adult,Adult,Swim Bladder,Swim Bladder