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
7948,ERR015562,ERX005932,ERS012705,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,,E MTAB 308:Zebrafish embryo 1 dpf 2,SAMEA898401,Wellcome Sanger Institute,Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. 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 resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation,E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 1 dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish embro 1 dpf mRNA three prime end,Zebrafish gene three prime end pull down for genome annotation,20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl.   RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin  magnetic beads.   post washing by pull down on a magnet  the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB.   post further washing  the double strand cDNA was released from the beads with BpmI NEB.   The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.,Experimental Factor: AGE:1 d|Experimental Factor: DEVELOPMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism|Experimental Factor: SEX:unknown sex,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000263,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation,ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16,3444_1.srf,srf,1358041568.0,8934484.0,E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 1 dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:376045982;C:281568469;G:271365867;T:407279179;N:21782071,76,76,,,376045982,281568469,271365867,407279179,21782071,ERX005932,ERS012705,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.94607,0.94542,0.3002,0.30139,0.73584,0.74038,0.51058,0.51233,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
35618,SRR32928249,SRX28203068,SRS24552774,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.H05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 8,78,78,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.H05.fq.gz,fastq,9110220.0,108455.0,expt2.broad.24.enzymatic.P01.H05.fq.gz,0:84,A:3384792;C:1565195;G:1973031;T:2182427;N:4775,84,,,,3384792,1565195,1973031,2182427,4775,SRX28203068,SRS24552774,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35619,SRR32928250,SRX28203067,SRS24552773,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.G05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 7,77,77,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.G05.fq.gz,fastq,4093068.0,48727.0,expt2.broad.24.enzymatic.P01.G05.fq.gz,0:84,A:1283703;C:801390;G:874961;T:1130908;N:2106,84,,,,1283703,801390,874961,1130908,2106,SRX28203067,SRS24552773,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35620,SRR32928251,SRX28203066,SRS24552772,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.F05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 6,76,76,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.F05.fq.gz,fastq,15414840.0,183510.0,expt2.broad.24.enzymatic.P01.F05.fq.gz,0:84,A:6868692;C:2274988;G:2950304;T:3312556;N:8300,84,,,,6868692,2274988,2950304,3312556,8300,SRX28203066,SRS24552772,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35621,SRR32928252,SRX28203065,SRS24552771,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.E05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 5,75,75,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.E05.fq.gz,fastq,7552440.0,89910.0,expt2.broad.24.enzymatic.P01.E05.fq.gz,0:84,A:2833004;C:1314546;G:1543833;T:1856906;N:4151,84,,,,2833004,1314546,1543833,1856906,4151,SRX28203065,SRS24552771,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35622,SRR32928253,SRX28203064,SRS24552770,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.D05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 4,74,74,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.D05.fq.gz,fastq,18449592.0,219638.0,expt2.broad.24.enzymatic.P01.D05.fq.gz,0:84,A:8110605;C:2781954;G:3613141;T:3933803;N:10089,84,,,,8110605,2781954,3613141,3933803,10089,SRX28203064,SRS24552770,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35623,SRR32928254,SRX28203063,SRS24552769,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.C05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 3,73,73,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.C05.fq.gz,fastq,5944344.0,70766.0,expt2.broad.24.enzymatic.P01.C05.fq.gz,0:84,A:2038886;C:1067891;G:1274553;T:1559956;N:3058,84,,,,2038886,1067891,1274553,1559956,3058,SRX28203063,SRS24552769,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35624,SRR32928255,SRX28203062,SRS24552768,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.B05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 2,72,72,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.B05.fq.gz,fastq,8608320.0,102480.0,expt2.broad.24.enzymatic.P01.B05.fq.gz,0:84,A:3054837;C:1594241;G:1754868;T:2199803;N:4571,84,,,,3054837,1594241,1754868,2199803,4571,SRX28203062,SRS24552768,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35625,SRR32928256,SRX28203061,SRS24552767,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.A05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 1,71,71,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.A05.fq.gz,fastq,3979164.0,47371.0,expt2.broad.24.enzymatic.P01.A05.fq.gz,0:84,A:1268971;C:764759;G:844472;T:1098812;N:2150,84,,,,1268971,764759,844472,1098812,2150,SRX28203061,SRS24552767,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35679,SRR32928309,SRX28203007,SRS24552713,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.D05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 4,145,145,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.D05.fq.gz,fastq,364669704.0,4341306.0,expt2.deep.24.enzymatic.P01.D05.fq.gz,0:84,A:165363989;C:53167919;G:71115587;T:74956203;N:66006,84,,,,165363989,53167919,71115587,74956203,66006,SRX28203007,SRS24552713,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35680,SRR32928311,SRX28203006,SRS24552711,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.C05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 3,144,144,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.C05.fq.gz,fastq,79366728.0,944842.0,expt2.deep.24.enzymatic.P01.C05.fq.gz,0:84,A:30604656;C:12612645;G:16345725;T:19789600;N:14102,84,,,,30604656,12612645,16345725,19789600,14102,SRX28203006,SRS24552711,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35681,SRR32928312,SRX28203005,SRS24552712,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.B05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 2,143,143,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.B05.fq.gz,fastq,124887084.0,1486751.0,expt2.deep.24.enzymatic.P01.B05.fq.gz,0:84,A:49284416;C:21398883;G:23939821;T:30241510;N:22454,84,,,,49284416,21398883,23939821,30241510,22454,SRX28203005,SRS24552712,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35682,SRR32928313,SRX28203004,SRS24552710,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.A05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 1,142,142,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.A05.fq.gz,fastq,48850200.0,581550.0,expt2.deep.24.enzymatic.P01.A05.fq.gz,0:84,A:17085857;C:8742596;G:9989085;T:13024179;N:8483,84,,,,17085857,8742596,9989085,13024179,8483,SRX28203004,SRS24552710,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35683,SRR32928314,SRX28203003,SRS24552709,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.H08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 15,141,141,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.H08.fq.gz,fastq,105747516.0,1258899.0,expt2.deep.24.bead.P18.H08.fq.gz,0:84,A:39780997;C:18282450;G:21178201;T:26487273;N:18595,84,,,,39780997,18282450,21178201,26487273,18595,SRX28203003,SRS24552709,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35685,SRR32928316,SRX28203001,SRS24552707,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.H07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 14,140,140,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.H07.fq.gz,fastq,117293568.0,1396352.0,expt2.deep.24.bead.P18.H07.fq.gz,0:84,A:44388972;C:20447464;G:23549662;T:28886998;N:20472,84,,,,44388972,20447464,23549662,28886998,20472,SRX28203001,SRS24552707,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35686,SRR32928317,SRX28203000,SRS24552706,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.G08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:13|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 13,139,139,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.G08.fq.gz,fastq,141454152.0,1683978.0,expt2.deep.24.bead.P18.G08.fq.gz,0:84,A:51351272;C:25274905;G:28542033;T:36261200;N:24742,84,,,,51351272,25274905,28542033,36261200,24742,SRX28203000,SRS24552706,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35687,SRR32928318,SRX28202999,SRS24552704,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.G07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:12|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 12,138,138,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.G07.fq.gz,fastq,122244864.0,1455296.0,expt2.deep.24.bead.P18.G07.fq.gz,0:84,A:45925081;C:20992270;G:24808169;T:30497807;N:21537,84,,,,45925081,20992270,24808169,30497807,21537,SRX28202999,SRS24552704,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35688,SRR32928319,SRX28202998,SRS24552705,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.F08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:11|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 11,137,137,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.F08.fq.gz,fastq,128994264.0,1535646.0,expt2.deep.24.bead.P18.F08.fq.gz,0:84,A:48283607;C:21968133;G:25901679;T:32817928;N:22917,84,,,,48283607,21968133,25901679,32817928,22917,SRX28202998,SRS24552705,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35689,SRR32928320,SRX28202997,SRS24552703,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.F07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 10,136,136,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.F07.fq.gz,fastq,118856724.0,1414961.0,expt2.deep.24.bead.P18.F07.fq.gz,0:84,A:43763583;C:20413885;G:24105737;T:30552660;N:20859,84,,,,43763583,20413885,24105737,30552660,20859,SRX28202997,SRS24552703,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35690,SRR32928321,SRX28202996,SRS24552702,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.E08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 9,135,135,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.E08.fq.gz,fastq,93617076.0,1114489.0,expt2.deep.24.bead.P18.E08.fq.gz,0:84,A:34570395;C:16556476;G:18475268;T:23998365;N:16572,84,,,,34570395,16556476,18475268,23998365,16572,SRX28202996,SRS24552702,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35691,SRR32928322,SRX28202995,SRS24552701,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.E07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 8,134,134,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.E07.fq.gz,fastq,133722792.0,1591938.0,expt2.deep.24.bead.P18.E07.fq.gz,0:84,A:50066403;C:23328616;G:26650458;T:33653419;N:23896,84,,,,50066403,23328616,26650458,33653419,23896,SRX28202995,SRS24552701,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35692,SRR32928323,SRX28202994,SRS24552699,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.D08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 7,133,133,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.D08.fq.gz,fastq,106928304.0,1272956.0,expt2.deep.24.bead.P18.D08.fq.gz,0:84,A:40254325;C:17917465;G:21658773;T:27078732;N:19009,84,,,,40254325,17917465,21658773,27078732,19009,SRX28202994,SRS24552699,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35693,SRR32928324,SRX28202993,SRS24552700,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.D07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 6,132,132,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.D07.fq.gz,fastq,178733856.0,2127784.0,expt2.deep.24.bead.P18.D07.fq.gz,0:84,A:71103187;C:30043845;G:34285236;T:43269649;N:31939,84,,,,71103187,30043845,34285236,43269649,31939,SRX28202993,SRS24552700,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35694,SRR32928325,SRX28202992,SRS24552698,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.C08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 5,131,131,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.C08.fq.gz,fastq,118834296.0,1414694.0,expt2.deep.24.bead.P18.C08.fq.gz,0:84,A:43351162;C:20642531;G:24057336;T:30762255;N:21012,84,,,,43351162,20642531,24057336,30762255,21012,SRX28202992,SRS24552698,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35696,SRR32928327,SRX28202990,SRS24552696,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.C07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 4,130,130,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.C07.fq.gz,fastq,83413848.0,993022.0,expt2.deep.24.bead.P18.C07.fq.gz,0:84,A:31147177;C:14298386;G:16802760;T:21150889;N:14636,84,,,,31147177,14298386,16802760,21150889,14636,SRX28202990,SRS24552696,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35697,SRR32928328,SRX28202989,SRS24552695,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.B08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 3,129,129,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.B08.fq.gz,fastq,110508132.0,1315573.0,expt2.deep.24.bead.P18.B08.fq.gz,0:84,A:41593318;C:19375759;G:21744173;T:27775466;N:19416,84,,,,41593318,19375759,21744173,27775466,19416,SRX28202989,SRS24552695,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35698,SRR32928329,SRX28202988,SRS24552694,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.B07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 2,128,128,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.B07.fq.gz,fastq,102579624.0,1221186.0,expt2.deep.24.bead.P18.B07.fq.gz,0:84,A:40321999;C:17087460;G:21685849;T:23466093;N:18223,84,,,,40321999,17087460,21685849,23466093,18223,SRX28202988,SRS24552694,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35699,SRR32928330,SRX28202987,SRS24552692,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.A08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 1,127,127,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.A08.fq.gz,fastq,108953208.0,1297062.0,expt2.deep.24.bead.P18.A08.fq.gz,0:84,A:40914540;C:18897489;G:22112695;T:27009444;N:19040,84,,,,40914540,18897489,22112695,27009444,19040,SRX28202987,SRS24552692,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35703,SRR32928334,SRX28202983,SRS24552689,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.H08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 15,70,70,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.H08.fq.gz,fastq,8144136.0,96954.0,expt2.broad.24.bead.P18.H08.fq.gz,0:84,A:2749870;C:1520663;G:1719585;T:2149644;N:4374,84,,,,2749870,1520663,1719585,2149644,4374,SRX28202983,SRS24552689,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35704,SRR32928335,SRX28202982,SRS24552687,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.H07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 14,69,69,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.H07.fq.gz,fastq,8916852.0,106153.0,expt2.broad.24.bead.P18.H07.fq.gz,0:84,A:3045003;C:1665942;G:1865766;T:2335320;N:4821,84,,,,3045003,1665942,1865766,2335320,4821,SRX28202982,SRS24552687,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35705,SRR32928336,SRX28202981,SRS24552688,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.G08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:13|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 13,68,68,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.G08.fq.gz,fastq,11133024.0,132536.0,expt2.broad.24.bead.P18.G08.fq.gz,0:84,A:3648380;C:2130637;G:2362380;T:2985637;N:5990,84,,,,3648380,2130637,2362380,2985637,5990,SRX28202981,SRS24552688,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35706,SRR32928337,SRX28202980,SRS24552686,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.G07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:12|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 12,67,67,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.G07.fq.gz,fastq,9315600.0,110900.0,expt2.broad.24.bead.P18.G07.fq.gz,0:84,A:3156213;C:1738465;G:1978549;T:2437568;N:4805,84,,,,3156213,1738465,1978549,2437568,4805,SRX28202980,SRS24552686,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35707,SRR32928338,SRX28202979,SRS24552685,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.F08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:11|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 11,66,66,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.F08.fq.gz,fastq,9789276.0,116539.0,expt2.broad.24.bead.P18.F08.fq.gz,0:84,A:3320270;C:1800281;G:2046649;T:2616905;N:5171,84,,,,3320270,1800281,2046649,2616905,5171,SRX28202979,SRS24552685,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35708,SRR32928339,SRX28202978,SRS24552684,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.F07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 10,65,65,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.F07.fq.gz,fastq,9214632.0,109698.0,expt2.broad.24.bead.P18.F07.fq.gz,0:84,A:3057793;C:1718213;G:1953657;T:2480102;N:4867,84,,,,3057793,1718213,1953657,2480102,4867,SRX28202978,SRS24552684,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35709,SRR32928340,SRX28202977,SRS24552682,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.E08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 9,64,64,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.E08.fq.gz,fastq,7261128.0,86442.0,expt2.broad.24.bead.P18.E08.fq.gz,0:84,A:2416194;C:1376949;G:1512433;T:1951817;N:3735,84,,,,2416194,1376949,1512433,1951817,3735,SRX28202977,SRS24552682,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35710,SRR32928341,SRX28202976,SRS24552683,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.E07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 8,63,63,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.E07.fq.gz,fastq,10062696.0,119794.0,expt2.broad.24.bead.P18.E07.fq.gz,0:84,A:3401117;C:1892628;G:2108920;T:2654785;N:5246,84,,,,3401117,1892628,2108920,2654785,5246,SRX28202976,SRS24552683,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35711,SRR32928342,SRX28202975,SRS24552681,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.D08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 7,62,62,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.D08.fq.gz,fastq,8198064.0,97596.0,expt2.broad.24.bead.P18.D08.fq.gz,0:84,A:2780756;C:1495133;G:1726582;T:2191139;N:4454,84,,,,2780756,1495133,1726582,2191139,4454,SRX28202975,SRS24552681,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35712,SRR32928343,SRX28202974,SRS24552680,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.D07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 6,61,61,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.D07.fq.gz,fastq,12509616.0,148924.0,expt2.broad.24.bead.P18.D07.fq.gz,0:84,A:4522316;C:2258311;G:2528248;T:3194042;N:6699,84,,,,4522316,2258311,2528248,3194042,6699,SRX28202974,SRS24552680,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35714,SRR32928345,SRX28202972,SRS24552677,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.C08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 5,60,60,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.C08.fq.gz,fastq,9391032.0,111798.0,expt2.broad.24.bead.P18.C08.fq.gz,0:84,A:3084926;C:1769610;G:1994555;T:2536912;N:5029,84,,,,3084926,1769610,1994555,2536912,5029,SRX28202972,SRS24552677,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35715,SRR32928346,SRX28202971,SRS24552678,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.C07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 4,59,59,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.C07.fq.gz,fastq,6317808.0,75212.0,expt2.broad.24.bead.P18.C07.fq.gz,0:84,A:2140905;C:1158658;G:1317321;T:1697538;N:3386,84,,,,2140905,1158658,1317321,1697538,3386,SRX28202971,SRS24552678,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35716,SRR32928347,SRX28202970,SRS24552676,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.B08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 3,58,58,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.B08.fq.gz,fastq,8412264.0,100146.0,expt2.broad.24.bead.P18.B08.fq.gz,0:84,A:2859217;C:1571503;G:1739845;T:2237036;N:4663,84,,,,2859217,1571503,1739845,2237036,4663,SRX28202970,SRS24552676,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35717,SRR32928348,SRX28202969,SRS24552675,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.B07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 2,57,57,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.B07.fq.gz,fastq,7301532.0,86923.0,expt2.broad.24.bead.P18.B07.fq.gz,0:84,A:2597215;C:1318665;G:1571260;T:1810507;N:3885,84,,,,2597215,1318665,1571260,1810507,3885,SRX28202969,SRS24552675,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35718,SRR32928349,SRX28202968,SRS24552674,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.A08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 1,56,56,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.A08.fq.gz,fastq,8205204.0,97681.0,expt2.broad.24.bead.P18.A08.fq.gz,0:84,A:2779647;C:1533064;G:1734713;T:2153264;N:4516,84,,,,2779647,1533064,1734713,2153264,4516,SRX28202968,SRS24552674,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35748,SRR32928380,SRX28202938,SRS24552644,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.H05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 8,149,149,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.H05.fq.gz,fastq,145976544.0,1737816.0,expt2.deep.24.enzymatic.P01.H05.fq.gz,0:84,A:60441236;C:22508438;G:31356971;T:31643952;N:25947,84,,,,60441236,22508438,31356971,31643952,25947,SRX28202938,SRS24552644,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35749,SRR32928381,SRX28202937,SRS24552643,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.G05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 7,148,148,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.G05.fq.gz,fastq,47683356.0,567659.0,expt2.deep.24.enzymatic.P01.G05.fq.gz,0:84,A:16326128;C:8784428;G:9655524;T:12908835;N:8441,84,,,,16326128,8784428,9655524,12908835,8441,SRX28202937,SRS24552643,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35750,SRR32928382,SRX28202936,SRS24552642,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.F05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 6,147,147,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.F05.fq.gz,fastq,277176648.0,3299722.0,expt2.deep.24.enzymatic.P01.F05.fq.gz,0:84,A:130211241;C:38031050;G:52145937;T:56738200;N:50220,84,,,,130211241,38031050,52145937,56738200,50220,SRX28202936,SRS24552642,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35751,SRR32928383,SRX28202935,SRS24552641,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.E05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 5,146,146,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.E05.fq.gz,fastq,118783980.0,1414095.0,expt2.deep.24.enzymatic.P01.E05.fq.gz,0:84,A:48417705;C:19064392;G:23595546;T:27685220;N:21117,84,,,,48417705,19064392,23595546,27685220,21117,SRX28202935,SRS24552641,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
36377,SRR499867,SRX148957,SRS334486,SRP013309,PRJNA167302,Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform,GSE38125,Other,Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.,,pubmed:23758687,,Dre 24h silver ions,GSM935119,,source name:Dre 24h silver ions|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver ions 0.25 µg/L of silver nitrate|barcode:GCTA,Dre 24h silver ions,FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library,Dre 24h silver ions,Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 µg/L of 10nm Ag NP  5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80°C for analysis of gene expression. The experiment was terminated at 48 hpf.,High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.,Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.,strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver ions 0.25 µg/L of silver nitrate|barcode:GCTA,GSM935119,GSM935119: Dre 24h silver ions; Danio rerio; OTHER,GSM935119 1,GSM935119: Dre 24h silver ions,1,,GEO Accession:GSM935119,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013309,,,Dre_24h_ag.gz,fastq,57745404.0,1604039.0,GSM935119 r1,0:36,A:11280863;C:17795869;G:15444087;T:13175334;N:49251,36,,,,11280863,17795869,15444087,13175334,49251,SRX148957,SRS334486,SRA053074,GEO,"van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter",1,0.10143,,0.00773,,0.96435,,0.60432,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,bulk,bulk,,United Kingdom,2012-05-22,Pharyngula,Embryo,Whole Organism,All anatomical structures
36378,SRR499866,SRX148956,SRS334485,SRP013309,PRJNA167302,Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform,GSE38125,Other,Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.,,pubmed:23758687,,Dre 24h silver bulk,GSM935118,,source name:Dre 24h silver bulk|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver bulk 0.6 1.6µm; 5 µg/L|barcode:GCTC,Dre 24h silver bulk,FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library,Dre 24h silver bulk,Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 µg/L of 10nm Ag NP  5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80°C for analysis of gene expression. The experiment was terminated at 48 hpf.,High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.,Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.,strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver bulk 0.6 1.6µm; 5 µg/L|barcode:GCTC,GSM935118,GSM935118: Dre 24h silver bulk; Danio rerio; OTHER,GSM935118 1,GSM935118: Dre 24h silver bulk,1,,GEO Accession:GSM935118,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013309,,,Dre_24h_bulk.gz,fastq,53296632.0,1480462.0,GSM935118 r1,0:36,A:8986044;C:17367907;G:13631579;T:13181001;N:130101,36,,,,8986044,17367907,13631579,13181001,130101,SRX148956,SRS334485,SRA053074,GEO,"van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter",1,0.078,,0.00708,,0.96877,,0.4609,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,bulk,bulk,,United Kingdom,2012-05-22,Pharyngula,Embryo,Whole Organism,All anatomical structures
36379,SRR499865,SRX148955,SRS334484,SRP013309,PRJNA167302,Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform,GSE38125,Other,Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.,,pubmed:23758687,,Dre 24h silver NP,GSM935117,,source name:Dre 24h silver NP|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver nanoparticles 10nm; 5µg/L|barcode:GCAG,Dre 24h silver NP,FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library,Dre 24h silver NP,Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 µg/L of 10nm Ag NP  5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80°C for analysis of gene expression. The experiment was terminated at 48 hpf.,High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.,Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.,strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver nanoparticles 10nm; 5µg/L|barcode:GCAG,GSM935117,GSM935117: Dre 24h silver NP; Danio rerio; OTHER,GSM935117 1,GSM935117: Dre 24h silver NP,1,,GEO Accession:GSM935117,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013309,,,Dre_24h_NP.gz,fastq,103827096.0,2884086.0,GSM935117 r1,0:36,A:22437552;C:29017806;G:28385826;T:23907583;N:78329,36,,,,22437552,29017806,28385826,23907583,78329,SRX148955,SRS334484,SRA053074,GEO,"van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter",1,0.16321,,0.01606,,0.94631,,0.45783,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,bulk,bulk,,United Kingdom,2012-05-22,Pharyngula,Embryo,Whole Organism,All anatomical structures
36380,SRR499864,SRX148954,SRS334483,SRP013309,PRJNA167302,Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform,GSE38125,Other,Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.,,pubmed:23758687,,Dre 24h control,GSM935116,,source name:Dre 24h control|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:control|barcode:GCAT,Dre 24h control,FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library,Dre 24h control,Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 µg/L of 10nm Ag NP  5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80°C for analysis of gene expression. The experiment was terminated at 48 hpf.,High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.,Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.,strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:control|barcode:GCAT,GSM935116,GSM935116: Dre 24h control; Danio rerio; OTHER,GSM935116 1,GSM935116: Dre 24h control,1,,GEO Accession:GSM935116,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013309,,,Dre_24h_control.gz,fastq,85032468.0,2362013.0,GSM935116 r1,0:36,A:16524315;C:24822030;G:21632275;T:21837611;N:216237,36,,,,16524315,24822030,21632275,21837611,216237,SRX148954,SRS334483,SRA053074,GEO,"van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter",1,0.13983,,0.01175,,0.95966,,0.52467,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,bulk,bulk,,United Kingdom,2012-05-22,Pharyngula,Embryo,Whole Organism,All anatomical structures
36542,SRR580559,SRX192121,SRS367419,SRP016009,PRJNA176710,Zebrafish Danio rerio catecholaminergic neuron RNA seq based transcript profiles,GSE41373,Transcriptome Analysis,This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish Danio rerio. Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24  36  72 hpf and 96 hpf  embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish. Overall design: Catecholaminergic neurons were labeled by four different strategies: 1 24 hrs old embryos: we used the ETvmat2:GFP transgenic line Wen et al. 2007. Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Dev Biol. 2008 Vol 314 p84 92 which at this early stage labels catecholaminergic neurons in posterior tuberculum and locus coeruleus; 2 24 hrs old embryos: we used Tgotpb.A:egfpzc48 transgenic line Fujimoto et al. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev Biol 2011  Vol 352  p393–404 which at this stage label ventral diencephalic dopaminergic neurons and some preoptic neurons. 3 For 72 and 96 hrs old zebrafish larvae we used a th:GFP BAC transgenic lines that labels catecholaminergic neurons Tay et al.  Comprehensive catecholaminergic projectome analysis reveals single neuron integration of zebrafish ascending and descending dopaminergic systems. Nat Comms 2011 Vol 2  171; also: T. Leng and W. Driever  unpublished. 4 for the 36 and 48 hrs old zebrafish larvae we used a th:Gal4VP16 driver and UAS:EGFP responder transgenic line system to label catecholaminergic cells Fernandes et al.  Deep brain photoreceptors control light seeking behavior in zebrafish larvae. Curr Biol. 2012 Vol 22  DOI 10.1016/j.cub.2012.08.016. We used the different transgenic lines  because lines 3 and 4 do not efficiently label catecholaminergic neurons at early stages  while lines 1 and 2 also have GFP expression in several other non catecholaminergic populations at later stages of development. Embryos were dissociated and catecholaminergic neurons were FACS sorted from GFP tagged zebrafish Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633. RNA was either processed for NanoCAGE  or mRNA was isolated and amplified. cDNA was sequenced by Illumina technique. This data submission is a series of data files consisting of three independent experiments with diffrent RNA Seq depth: Samples 1 4 NanoCage: Samples 5 8 RNA Seq high read numbers  and SAmples 9 12 RNA Seq low read numbers.,,,,otpb:GFP 24h GFPplus sorted catecholaminergic neurons,GSM1015801,,tissue:FACS sorted cells from whole embryo|developmental stage:24 hpf line:Tgotpb.A:egfpzc48|facs sorting criteria:GFP positive cells,otpb:GFP 24h GFPplus sorted catecholaminergic neurons,"Library strategy: RNA Seq NanoCAGE Illumina Casava1.7 software used for basecalling. Samples 1 through 4: sequence data are in read files from two lanes using bar codes vmatGFPminus   ATCGTG; vmatGFPplus   AGTATA; otpGFPminus   AGTAGC; otpGFPplus   AGTACG; Samples 5 though 12 sequence data are in separate read files each Fastq sequencing data  were imported with NGS Illumina import. For this import the quality score was set to “Illumina pipline 1.5 to 1.7” Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using CLC Genomics Workbench v4.8 Sequences were mapped to genome with CLC Genomics Workbench v4.8 built48014 using menue ""high thriughput sequencing"" and mapping settings minimal fraction length 0.9  minimum similarity fraction 0.8  maximum number of hitts for read 10 Expression values were calculated as RPKM using CLC Genomics Workbench v4.8 Statistical analysis were performed using the Test on proportions => Kal et al.‘s test Z test using CLC Genomics Workbench v4.8 Genome build: Zebrafish reference genome ZV9.66 Supplementary files format and content: Excel spreadsheets with output generated from CLC Genomics Workbench v4.8; each spreadsheet  provides data analysis for comparison of one GFP plus experimental and one GFP minus control sample",FACS sorted cells from whole embryo,Cells were dissociated and FACS sorted as described in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633,RNA was extracted from FACS sorted cells as descried in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 Samples 1 through 4 were processed for NanoCAGE Salmullah et al.  CSH Protocols 2011  DOI 10.1101/pdb.prot5559; Samples 5 through 12 were processed for mRNA Seq Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 including an amplification step using Ambion RNA amp kit as described in CSH Protocol.,Zebrafish were gown under standard condition 28 Celsius,developmental stage:24 hpf line:Tgotpb.A:egfpzc48|facs sorting criteria:GFP positive cells,GSM1015801,GSM1015801: otpb:GFP 24h GFPplus sorted catecholaminergic neurons; Danio rerio; OTHER,GSM1015801 1,,1,,GEO Accession:GSM1015801,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP016009,,,Sample_4_MM_otpb_GFP_24h_GFPplus_Barcode_AGTACG.txt,fastq,50452590.0,1681753.0,GSM1015801 r1,0:30,A:10849523;C:10278613;G:20054813;T:9269193;N:448,30,,,,10849523,10278613,20054813,9269193,448,SRX192121,SRS367419,SRA059310,GEO,"Developmental Biology, Biology, University of Freiburg",1,0.71246,,0.18481,,0.88625,,0.78452,,30,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2012-10-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
36543,SRR580558,SRX192120,SRS367418,SRP016009,PRJNA176710,Zebrafish Danio rerio catecholaminergic neuron RNA seq based transcript profiles,GSE41373,Transcriptome Analysis,This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish Danio rerio. Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24  36  72 hpf and 96 hpf  embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish. Overall design: Catecholaminergic neurons were labeled by four different strategies: 1 24 hrs old embryos: we used the ETvmat2:GFP transgenic line Wen et al. 2007. Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Dev Biol. 2008 Vol 314 p84 92 which at this early stage labels catecholaminergic neurons in posterior tuberculum and locus coeruleus; 2 24 hrs old embryos: we used Tgotpb.A:egfpzc48 transgenic line Fujimoto et al. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev Biol 2011  Vol 352  p393–404 which at this stage label ventral diencephalic dopaminergic neurons and some preoptic neurons. 3 For 72 and 96 hrs old zebrafish larvae we used a th:GFP BAC transgenic lines that labels catecholaminergic neurons Tay et al.  Comprehensive catecholaminergic projectome analysis reveals single neuron integration of zebrafish ascending and descending dopaminergic systems. Nat Comms 2011 Vol 2  171; also: T. Leng and W. Driever  unpublished. 4 for the 36 and 48 hrs old zebrafish larvae we used a th:Gal4VP16 driver and UAS:EGFP responder transgenic line system to label catecholaminergic cells Fernandes et al.  Deep brain photoreceptors control light seeking behavior in zebrafish larvae. Curr Biol. 2012 Vol 22  DOI 10.1016/j.cub.2012.08.016. We used the different transgenic lines  because lines 3 and 4 do not efficiently label catecholaminergic neurons at early stages  while lines 1 and 2 also have GFP expression in several other non catecholaminergic populations at later stages of development. Embryos were dissociated and catecholaminergic neurons were FACS sorted from GFP tagged zebrafish Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633. RNA was either processed for NanoCAGE  or mRNA was isolated and amplified. cDNA was sequenced by Illumina technique. This data submission is a series of data files consisting of three independent experiments with diffrent RNA Seq depth: Samples 1 4 NanoCage: Samples 5 8 RNA Seq high read numbers  and SAmples 9 12 RNA Seq low read numbers.,,,,otpb:GFP 24h GFPminus control,GSM1015800,,tissue:FACS sorted cells from whole embryo|developmental stage:24 hpf line:Tgotpb.A:egfpzc48|facs sorting criteria:GFP negative cells,otpb:GFP 24h GFPminus control,"Library strategy: RNA Seq NanoCAGE Illumina Casava1.7 software used for basecalling. Samples 1 through 4: sequence data are in read files from two lanes using bar codes vmatGFPminus   ATCGTG; vmatGFPplus   AGTATA; otpGFPminus   AGTAGC; otpGFPplus   AGTACG; Samples 5 though 12 sequence data are in separate read files each Fastq sequencing data  were imported with NGS Illumina import. For this import the quality score was set to “Illumina pipline 1.5 to 1.7” Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using CLC Genomics Workbench v4.8 Sequences were mapped to genome with CLC Genomics Workbench v4.8 built48014 using menue ""high thriughput sequencing"" and mapping settings minimal fraction length 0.9  minimum similarity fraction 0.8  maximum number of hitts for read 10 Expression values were calculated as RPKM using CLC Genomics Workbench v4.8 Statistical analysis were performed using the Test on proportions => Kal et al.‘s test Z test using CLC Genomics Workbench v4.8 Genome build: Zebrafish reference genome ZV9.66 Supplementary files format and content: Excel spreadsheets with output generated from CLC Genomics Workbench v4.8; each spreadsheet  provides data analysis for comparison of one GFP plus experimental and one GFP minus control sample",FACS sorted cells from whole embryo,Cells were dissociated and FACS sorted as described in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633,RNA was extracted from FACS sorted cells as descried in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 Samples 1 through 4 were processed for NanoCAGE Salmullah et al.  CSH Protocols 2011  DOI 10.1101/pdb.prot5559; Samples 5 through 12 were processed for mRNA Seq Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 including an amplification step using Ambion RNA amp kit as described in CSH Protocol.,Zebrafish were gown under standard condition 28 Celsius,developmental stage:24 hpf line:Tgotpb.A:egfpzc48|facs sorting criteria:GFP negative cells,GSM1015800,GSM1015800: otpb:GFP 24h GFPminus control; Danio rerio; OTHER,GSM1015800 1,,1,,GEO Accession:GSM1015800,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP016009,,,,,131819610.0,4393987.0,GSM1015800 r1,0:30,A:27390381;C:27017723;G:54003025;T:23407312;N:1169,30,,,,27390381,27017723,54003025,23407312,1169,SRX192120,SRS367418,SRA059310,GEO,"Developmental Biology, Biology, University of Freiburg",1,0.81684,,0.24841,,0.9082,,0.95244,,30,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2012-10-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
36544,SRR580557,SRX192119,SRS367417,SRP016009,PRJNA176710,Zebrafish Danio rerio catecholaminergic neuron RNA seq based transcript profiles,GSE41373,Transcriptome Analysis,This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish Danio rerio. Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24  36  72 hpf and 96 hpf  embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish. Overall design: Catecholaminergic neurons were labeled by four different strategies: 1 24 hrs old embryos: we used the ETvmat2:GFP transgenic line Wen et al. 2007. Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Dev Biol. 2008 Vol 314 p84 92 which at this early stage labels catecholaminergic neurons in posterior tuberculum and locus coeruleus; 2 24 hrs old embryos: we used Tgotpb.A:egfpzc48 transgenic line Fujimoto et al. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev Biol 2011  Vol 352  p393–404 which at this stage label ventral diencephalic dopaminergic neurons and some preoptic neurons. 3 For 72 and 96 hrs old zebrafish larvae we used a th:GFP BAC transgenic lines that labels catecholaminergic neurons Tay et al.  Comprehensive catecholaminergic projectome analysis reveals single neuron integration of zebrafish ascending and descending dopaminergic systems. Nat Comms 2011 Vol 2  171; also: T. Leng and W. Driever  unpublished. 4 for the 36 and 48 hrs old zebrafish larvae we used a th:Gal4VP16 driver and UAS:EGFP responder transgenic line system to label catecholaminergic cells Fernandes et al.  Deep brain photoreceptors control light seeking behavior in zebrafish larvae. Curr Biol. 2012 Vol 22  DOI 10.1016/j.cub.2012.08.016. We used the different transgenic lines  because lines 3 and 4 do not efficiently label catecholaminergic neurons at early stages  while lines 1 and 2 also have GFP expression in several other non catecholaminergic populations at later stages of development. Embryos were dissociated and catecholaminergic neurons were FACS sorted from GFP tagged zebrafish Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633. RNA was either processed for NanoCAGE  or mRNA was isolated and amplified. cDNA was sequenced by Illumina technique. This data submission is a series of data files consisting of three independent experiments with diffrent RNA Seq depth: Samples 1 4 NanoCage: Samples 5 8 RNA Seq high read numbers  and SAmples 9 12 RNA Seq low read numbers.,,,,vmat2:GFP 24h GFPplus sorted catecholaminergic neurons,GSM1015799,,tissue:FACS sorted cells from whole embryo|developmental stage:24 hpf line:ETvmat2:GFP|facs sorting criteria:GFP positive cells,vmat2:GFP 24h GFPplus sorted catecholaminergic neurons,"Library strategy: RNA Seq NanoCAGE Illumina Casava1.7 software used for basecalling. Samples 1 through 4: sequence data are in read files from two lanes using bar codes vmatGFPminus   ATCGTG; vmatGFPplus   AGTATA; otpGFPminus   AGTAGC; otpGFPplus   AGTACG; Samples 5 though 12 sequence data are in separate read files each Fastq sequencing data  were imported with NGS Illumina import. For this import the quality score was set to “Illumina pipline 1.5 to 1.7” Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using CLC Genomics Workbench v4.8 Sequences were mapped to genome with CLC Genomics Workbench v4.8 built48014 using menue ""high thriughput sequencing"" and mapping settings minimal fraction length 0.9  minimum similarity fraction 0.8  maximum number of hitts for read 10 Expression values were calculated as RPKM using CLC Genomics Workbench v4.8 Statistical analysis were performed using the Test on proportions => Kal et al.‘s test Z test using CLC Genomics Workbench v4.8 Genome build: Zebrafish reference genome ZV9.66 Supplementary files format and content: Excel spreadsheets with output generated from CLC Genomics Workbench v4.8; each spreadsheet  provides data analysis for comparison of one GFP plus experimental and one GFP minus control sample",FACS sorted cells from whole embryo,Cells were dissociated and FACS sorted as described in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633,RNA was extracted from FACS sorted cells as descried in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 Samples 1 through 4 were processed for NanoCAGE Salmullah et al.  CSH Protocols 2011  DOI 10.1101/pdb.prot5559; Samples 5 through 12 were processed for mRNA Seq Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 including an amplification step using Ambion RNA amp kit as described in CSH Protocol.,Zebrafish were gown under standard condition 28 Celsius,developmental stage:24 hpf line:ETvmat2:GFP|facs sorting criteria:GFP positive cells,GSM1015799,GSM1015799: vmat2:GFP 24h GFPplus sorted catecholaminergic neurons; Danio rerio; OTHER,GSM1015799 1,,1,,GEO Accession:GSM1015799,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP016009,,,,,89312790.0,2977093.0,GSM1015799 r1,0:30,A:19953403;C:17739114;G:34684963;T:16934433;N:877,30,,,,19953403,17739114,34684963,16934433,877,SRX192119,SRS367417,SRA059310,GEO,"Developmental Biology, Biology, University of Freiburg",1,0.66653,,0.18449,,0.87623,,0.81483,,30,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2012-10-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
36545,SRR580556,SRX192118,SRS367416,SRP016009,PRJNA176710,Zebrafish Danio rerio catecholaminergic neuron RNA seq based transcript profiles,GSE41373,Transcriptome Analysis,This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish Danio rerio. Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24  36  72 hpf and 96 hpf  embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish. Overall design: Catecholaminergic neurons were labeled by four different strategies: 1 24 hrs old embryos: we used the ETvmat2:GFP transgenic line Wen et al. 2007. Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Dev Biol. 2008 Vol 314 p84 92 which at this early stage labels catecholaminergic neurons in posterior tuberculum and locus coeruleus; 2 24 hrs old embryos: we used Tgotpb.A:egfpzc48 transgenic line Fujimoto et al. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev Biol 2011  Vol 352  p393–404 which at this stage label ventral diencephalic dopaminergic neurons and some preoptic neurons. 3 For 72 and 96 hrs old zebrafish larvae we used a th:GFP BAC transgenic lines that labels catecholaminergic neurons Tay et al.  Comprehensive catecholaminergic projectome analysis reveals single neuron integration of zebrafish ascending and descending dopaminergic systems. Nat Comms 2011 Vol 2  171; also: T. Leng and W. Driever  unpublished. 4 for the 36 and 48 hrs old zebrafish larvae we used a th:Gal4VP16 driver and UAS:EGFP responder transgenic line system to label catecholaminergic cells Fernandes et al.  Deep brain photoreceptors control light seeking behavior in zebrafish larvae. Curr Biol. 2012 Vol 22  DOI 10.1016/j.cub.2012.08.016. We used the different transgenic lines  because lines 3 and 4 do not efficiently label catecholaminergic neurons at early stages  while lines 1 and 2 also have GFP expression in several other non catecholaminergic populations at later stages of development. Embryos were dissociated and catecholaminergic neurons were FACS sorted from GFP tagged zebrafish Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633. RNA was either processed for NanoCAGE  or mRNA was isolated and amplified. cDNA was sequenced by Illumina technique. This data submission is a series of data files consisting of three independent experiments with diffrent RNA Seq depth: Samples 1 4 NanoCage: Samples 5 8 RNA Seq high read numbers  and SAmples 9 12 RNA Seq low read numbers.,,,,vmat2:GFP 24h GFPminus control,GSM1015798,,tissue:FACS sorted cells from whole embryo|developmental stage:24 hpf line:ETvmat2:GFP|facs sorting criteria:GFP negative cells,vmat2:GFP 24h GFPminus control,"Library strategy: RNA Seq NanoCAGE Illumina Casava1.7 software used for basecalling. Samples 1 through 4: sequence data are in read files from two lanes using bar codes vmatGFPminus   ATCGTG; vmatGFPplus   AGTATA; otpGFPminus   AGTAGC; otpGFPplus   AGTACG; Samples 5 though 12 sequence data are in separate read files each Fastq sequencing data  were imported with NGS Illumina import. For this import the quality score was set to “Illumina pipline 1.5 to 1.7” Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using CLC Genomics Workbench v4.8 Sequences were mapped to genome with CLC Genomics Workbench v4.8 built48014 using menue ""high thriughput sequencing"" and mapping settings minimal fraction length 0.9  minimum similarity fraction 0.8  maximum number of hitts for read 10 Expression values were calculated as RPKM using CLC Genomics Workbench v4.8 Statistical analysis were performed using the Test on proportions => Kal et al.‘s test Z test using CLC Genomics Workbench v4.8 Genome build: Zebrafish reference genome ZV9.66 Supplementary files format and content: Excel spreadsheets with output generated from CLC Genomics Workbench v4.8; each spreadsheet  provides data analysis for comparison of one GFP plus experimental and one GFP minus control sample",FACS sorted cells from whole embryo,Cells were dissociated and FACS sorted as described in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633,RNA was extracted from FACS sorted cells as descried in: Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 Samples 1 through 4 were processed for NanoCAGE Salmullah et al.  CSH Protocols 2011  DOI 10.1101/pdb.prot5559; Samples 5 through 12 were processed for mRNA Seq Manoli and Driever  2012  Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633 including an amplification step using Ambion RNA amp kit as described in CSH Protocol.,Zebrafish were gown under standard condition 28 Celsius,developmental stage:24 hpf line:ETvmat2:GFP|facs sorting criteria:GFP negative cells,GSM1015798,GSM1015798: vmat2:GFP 24h GFPminus control; Danio rerio; OTHER,GSM1015798 1,,1,,GEO Accession:GSM1015798,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP016009,,,,,109437330.0,3647911.0,GSM1015798 r1,0:30,A:22965140;C:22637764;G:44598580;T:19234832;N:1014,30,,,,22965140,22637764,44598580,19234832,1014,SRX192118,SRS367416,SRA059310,GEO,"Developmental Biology, Biology, University of Freiburg",1,0.79599,,0.21065,,0.90658,,0.9542,,30,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2012-10-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
40215,SRR2982514,SRX1471724,SRS1197482,SRP067139,PRJNA305418,RiboZero mRNA seq across zebrafish development  for study of uORFs,PRJNA305418,Other,Untranslated mRNA regionsUTRs are key mediators of post transcriptional regulation. Previous studies have predicted thousands of ORFs in five prime'UTRs  the vast majority of which have unknown function. We present a systematic analysis of the translation and function of upstream open reading framesuORFs across vertebrates. Combining high resolution ribosome footprinting and phasing  we find that i uORFs are pervasive within vertebrate transcriptomes  ii the majority show signatures of active translation  and iii uORFs act as potent regulators of translation and RNA levels  with a similar magnitude to miRNAs. Evolution has targeted sequence features to mitigate the effects of constitutively repressive uORFs. Finally  we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.The mRNA seq data contained in this archive were used along with ribosome profiling data to calculate translation efficiency values.,,,,24hpf,AG00750 mrna r0 24h,,strain:TUAB|age:24hpf|sex:pooled male and female|tissue:embryo|genotype:wt|BioSampleModel:Model organism or animal,,,,,,,,,AG00750 mrna r0 24h,24h mRNA R0,1,Twenty embryos per condition were collected from the same clutch from where the ribosome profiling timeseries was conducted.Bazzini et al  2014 Total RNA was isolated using 1mL of Trizol following manufacturer instructions. Ribosomal RNAs were depleted using Ribo Zero Epicentre/Illumina. Strand specific  single end library was constructed according to the Illumina Sample Preparation Kit protocol using standard TruSeq adapters Libraries were prepared and sequenced in an Illumina Hi SEQ  single end  75nt reads,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP067139,,,AG00750_SEQ0114_R1.fastq.gz,fastq,2124277824.0,27951024.0,24h mRNA R0 run1,0:76,A:537946274;C:496576029;G:477023623;T:612576823;N:155075,76,,,,537946274,496576029,477023623,612576823,155075,SRX1471724,SRS1197482,SRA314809,Yale University|Giraldez Lab,Yale University,1,0.86054,,0.27207,,0.69877,,0.47063,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,United States,2015-12-08,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
41511,SRR5004963,SRX2336797,SRS1790193,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,zebrafish embryos ythdf2 RIP rep2,GSM2386192,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,zebrafish embryos ythdf2 RIP rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software,zebrafish embryos,,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,GSM2386192,GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq,GSM2386192,,1,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386192,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz,fastq fastq,4007024510.0,19836755.0,GSM2386192 r1,0:101 1:101,A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309,101,101,,,769487104,1245093129,1251328145,740377823,738309,SRX2336797,SRS1790193,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.97768,0.97802,0.22786,0.21743,0.89885,0.89968,0.77584,0.83808,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41512,SRR5004962,SRX2336796,SRS1790194,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,zebrafish embryos ythdf2 RIP rep1,GSM2386191,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,zebrafish embryos ythdf2 RIP rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software,zebrafish embryos,,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,GSM2386191,GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq,GSM2386191,,1,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386191,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP092907,,,ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz,fastq fastq,6144583662.0,30418731.0,GSM2386191 r1,0:101 1:101,A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305,101,101,,,1227614258,1869131844,1825793436,1220118819,1925305,SRX2336796,SRS1790194,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.96857,0.96917,0.23397,0.22377,0.89832,0.90147,0.78619,0.8258,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41521,SRR5004953,SRX2336787,SRS1790184,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,mettl3 morphant zebrafish embryos m6A IP rep2,GSM2386182,,source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems,mettl3 morphant zebrafish embryos m6A IP rep2,Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples,zebrafish embryos,,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems,GSM2386182,GSM2386182: mettl3 morphant zebrafish embryos m6A IP rep2; Danio rerio; OTHER,GSM2386182,,1,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386182,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,mettl3-mo_IP_rep2_1.fastq.gz mettl3-mo_IP_rep2_2.fastq.gz,fastq fastq,12246129204.0,60624402.0,GSM2386182 r1,0:101 1:101,A:3253814653;C:2887966071;G:2921051332;T:3179545005;N:3752143,101,101,,,3253814653,2887966071,2921051332,3179545005,3752143,SRX2336787,SRS1790184,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.93906,0.94462,0.08073,0.07972,0.69148,0.69394,0.43224,0.48778,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41522,SRR5004952,SRX2336785,SRS1790183,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,mettl3 morphant zebrafish embryos m6A IP rep1,GSM2386181,,source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems,mettl3 morphant zebrafish embryos m6A IP rep1,Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples,zebrafish embryos,,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.,,genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems,GSM2386181,GSM2386181: mettl3 morphant zebrafish embryos m6A IP rep1; Danio rerio; OTHER,GSM2386181,,1,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.,GEO Accession:GSM2386181,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,mettl3-mo_IP_rep1_1.fastq.gz mettl3-mo_IP_rep1_2.fastq.gz,fastq fastq,22767872412.0,75390306.0,GSM2386181 r1,0:151 1:151,A:6356270201;C:5175380564;G:5545741592;T:5686194578;N:4285477,151,151,,,6356270201,5175380564,5545741592,5686194578,4285477,SRX2336785,SRS1790183,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.94647,0.95162,0.07314,0.07248,0.70796,0.71021,0.54859,0.54624,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41523,SRR5004951,SRX2336784,SRS1790182,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,control zebrafish embryos input rep2,GSM2386180,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,control zebrafish embryos input rep2,Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples,zebrafish embryos,,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,GSM2386180,GSM2386180: control zebrafish embryos input rep2; Danio rerio; OTHER,GSM2386180,,1,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386180,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,control_input_rep2_1.fastq.gz control_input_rep2_2.fastq.gz,fastq fastq,20629042748.0,102123974.0,GSM2386180 r1,0:101 1:101,A:5541548211;C:4810650367;G:4699999124;T:5571342766;N:5502280,101,101,,,5541548211,4810650367,4699999124,5571342766,5502280,SRX2336784,SRS1790182,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.94898,0.9511,0.10842,0.10266,0.70465,0.70481,0.4986,0.48915,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41524,SRR5004950,SRX2336783,SRS1790181,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,control zebrafish embryos input rep1,GSM2386179,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,control zebrafish embryos input rep1,Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples,zebrafish embryos,,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,GSM2386179,GSM2386179: control zebrafish embryos input rep1; Danio rerio; OTHER,GSM2386179,,1,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.,GEO Accession:GSM2386179,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,control_input_rep1_1.fastq.gz control_input_rep1_2.fastq.gz,fastq fastq,27776308060.0,91974530.0,GSM2386179 r1,0:151 1:151,A:7467418896;C:6517753701;G:6333567394;T:7452805069;N:4763000,151,151,,,7467418896,6517753701,6333567394,7452805069,4763000,SRX2336783,SRS1790181,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.95616,0.95939,0.10401,0.09776,0.72263,0.73637,0.57906,0.58185,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41525,SRR5004949,SRX2336782,SRS1790180,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,control zebrafish embryos m6A IP rep2,GSM2386178,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems,control zebrafish embryos m6A IP rep2,Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples,zebrafish embryos,,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems,GSM2386178,GSM2386178: control zebrafish embryos m6A IP rep2; Danio rerio; OTHER,GSM2386178,,1,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386178,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,control_IP_rep2_1.fastq.gz control_IP_rep2_2.fastq.gz,fastq fastq,11899573964.0,58908782.0,GSM2386178 r1,0:101 1:101,A:3146907590;C:2817914269;G:2838718195;T:3092392965;N:3640945,101,101,,,3146907590,2817914269,2838718195,3092392965,3640945,SRX2336782,SRS1790180,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.93821,0.94281,0.08361,0.08174,0.69676,0.69816,0.4628,0.46386,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41526,SRR5004948,SRX2336781,SRS1790179,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,control zebrafish embryos m6A IP rep1,GSM2386177,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems,control zebrafish embryos m6A IP rep1,Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples,zebrafish embryos,,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems,GSM2386177,GSM2386177: control zebrafish embryos m6A IP rep1; Danio rerio; OTHER,GSM2386177,,1,For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.,GEO Accession:GSM2386177,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,control_IP_rep1_1.fastq.gz control_IP_rep1_2.fastq.gz,fastq fastq,16582066208.0,54907504.0,GSM2386177 r1,0:151 1:151,A:4529890968;C:3812739433;G:4031512714;T:4204817283;N:3105810,151,151,,,4529890968,3812739433,4031512714,4204817283,3105810,SRX2336781,SRS1790179,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.93701,0.95377,0.07009,0.07008,0.70972,0.71173,0.54711,0.54995,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41527,SRR5441898,SRX2731753,SRS2119651,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,control zebrafish embryos m6A miCLIP rep2,GSM2572320,,source name:zebrafish embryos|cell type:normal zebrafish embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Abcam,control zebrafish embryos m6A miCLIP rep2,library strategy: miCLIP seq Reads were trimmed for adaptor sequence using fastx clipper from FASTX Toolkit fastx clipper  a AGATCGGAAGAGCACACG  n  Q 33. Low quality bases were filtered by fastq filter.pl  a custom perl script from CLIP Tool Kit CTK and reads shorter than 24 nt would be discard. The forward reads were demultiplexed based on 5’ barcodes for individual replicates by fastq2collapse.pl to remove PCR amplified reads. The reverse reads were reversed complemented and processed like their forward mates. And then paired end reads were mixed for downstream analysis. Random barcodes of remained reads were stripped by stripBarcode.pl. Then the barcode sequence was moved to header line for each read. Remained reads were mapped to the zebrafish genomes version zv9 with BWA v0.7.10. The CIMS pipeline https://zhanglab.c2b2.columbia.edu/index.php/CTK Documentation was used to collapse PCR duplicates based on their mapped coordinates and to determine the unique tag coverage k and the number of mutation m for each nucleotide. The filter for the dataset was k >= 15 and m/k <= 50% and only mutation positions within RRACH motif were identified as m6A for downstream analysis to exclude the potential m6Am modification. Genome build: zv9 Supplementary files format and content: Single nucleotide resolution m6A sites identified by CIMS software.,zebrafish embryos,,For miCLIP seq  mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,cell type:normal zebrafish embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Abcam,GSM2572320,GSM2572320: control zebrafish embryos m6A miCLIP rep2; Danio rerio; OTHER,GSM2572320,,1,For miCLIP seq  mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq2000 or HiSeq3000 Illumina in single read or paired read mode  creating reads with a length of 101 bp,GEO Accession:GSM2572320,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,miCLIP_Abcam_rep2_1.fastq.gz miCLIP_Abcam_rep2_2.fastq.gz,fastq fastq,5381144865.0,26771865.0,GSM2572320 r1,0:101 1:100,A:1590037266;C:1121098903;G:1187084038;T:1482144584;N:780074,101,100,,,1590037266,1121098903,1187084038,1482144584,780074,SRX2731753,SRS2119651,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.55442,0.60543,0.10037,0.11559,0.75432,0.747,0.55512,0.44818,101,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,clip,iclip,,China,2017-04-10,Pharyngula,Embryo,Trunk,Surface Structure
41528,SRR5441897,SRX2731752,SRS2119650,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,control zebrafish embryos m6A miCLIP rep1,GSM2572319,,source name:zebrafish embryos|cell type:normal zebrafish embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Abcam,control zebrafish embryos m6A miCLIP rep1,library strategy: miCLIP seq Reads were trimmed for adaptor sequence using fastx clipper from FASTX Toolkit fastx clipper  a AGATCGGAAGAGCACACG  n  Q 33. Low quality bases were filtered by fastq filter.pl  a custom perl script from CLIP Tool Kit CTK and reads shorter than 24 nt would be discard. The forward reads were demultiplexed based on 5’ barcodes for individual replicates by fastq2collapse.pl to remove PCR amplified reads. The reverse reads were reversed complemented and processed like their forward mates. And then paired end reads were mixed for downstream analysis. Random barcodes of remained reads were stripped by stripBarcode.pl. Then the barcode sequence was moved to header line for each read. Remained reads were mapped to the zebrafish genomes version zv9 with BWA v0.7.10. The CIMS pipeline https://zhanglab.c2b2.columbia.edu/index.php/CTK Documentation was used to collapse PCR duplicates based on their mapped coordinates and to determine the unique tag coverage k and the number of mutation m for each nucleotide. The filter for the dataset was k >= 15 and m/k <= 50% and only mutation positions within RRACH motif were identified as m6A for downstream analysis to exclude the potential m6Am modification. Genome build: zv9 Supplementary files format and content: Single nucleotide resolution m6A sites identified by CIMS software.,zebrafish embryos,,For miCLIP seq  mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,cell type:normal zebrafish embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Abcam,GSM2572319,GSM2572319: control zebrafish embryos m6A miCLIP rep1; Danio rerio; OTHER,GSM2572319,,1,For miCLIP seq  mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq2000 or HiSeq3000 Illumina in single read or paired read mode  creating reads with a length of 101 bp,GEO Accession:GSM2572319,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,miCLIP_Abcam_rep1_1.fastq.gz miCLIP_Abcam_rep1_2.fastq.gz,fastq fastq,6036174318.0,30030718.0,GSM2572319 r1,0:101 1:100,A:1726466495;C:1297674104;G:1364186585;T:1647084426;N:762708,101,100,,,1726466495,1297674104,1364186585,1647084426,762708,SRX2731752,SRS2119650,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.5985,0.66835,0.09404,0.1086,0.74491,0.73596,0.54343,0.45047,101,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,clip,iclip,,China,2017-04-10,Pharyngula,Embryo,Trunk,Surface Structure
42000,SRR5379364,SRX2674572,SRS2073700,SRP102513,PRJNA380609,Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing,GSE97067,Other,DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development  we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.,,pubmed:29636379,,ddx39a 24hpf RIPseq,GSM2550918,,source name:embryos|genotype:ddx39a mutant|tissue:embryo|developmental stage:24hpf,ddx39a 24hpf RIPseq,Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample,embryos,,Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.,,genotype:ddx39a mutant|tissue:embryo|developmental stage:24hpf,GSM2550918,GSM2550918: ddx39a 24hpf RIPseq; Danio rerio; RIP Seq,GSM2550918,,1,Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.,GEO Accession:GSM2550918,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP102513,,,RDWHDANwwwCAABRAAPEI-206_1.fq.gz RDWHDANwwwCAABRAAPEI-206_2.fq.gz,fastq fastq,3819239400.0,19096197.0,GSM2550918 r1,0:100 1:100,A:751858949;C:1169790479;G:1139713624;T:756987876;N:888472,100,100,,,751858949,1169790479,1139713624,756987876,888472,SRX2674572,SRS2073700,SRA549449,GEO,"Xin Lou Lab, Medical School, Nanjing University",2,0.98659,0.98572,0.28836,0.28975,0.89422,0.89558,0.75396,0.78553,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2017-03-27,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
42001,SRR5379363,SRX2674571,SRS2073697,SRP102513,PRJNA380609,Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing,GSE97067,Other,DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development  we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.,,pubmed:29636379,,WT 24hpf RIPseq,GSM2550917,,source name:embryos|genotype:wild type|tissue:embryo|developmental stage:24hpf,WT 24hpf RIPseq,Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample,embryos,,Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.,,genotype:wild type|tissue:embryo|developmental stage:24hpf,GSM2550917,GSM2550917: WT 24hpf RIPseq; Danio rerio; RIP Seq,GSM2550917,,1,Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.,GEO Accession:GSM2550917,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP102513,,,RDWHDANwwwCAAARAAPEI-205_2.fq.gz RDWHDANwwwCAAARAAPEI-205_1.fq.gz,fastq fastq,3802882200.0,19014411.0,GSM2550917 r1,0:100 1:100,A:733911232;C:1178365174;G:1154031422;T:735690235;N:884137,100,100,,,733911232,1178365174,1154031422,735690235,884137,SRX2674571,SRS2073697,SRA549449,GEO,"Xin Lou Lab, Medical School, Nanjing University",2,0.9866,0.98469,0.30567,0.30486,0.90796,0.90928,0.82926,0.83029,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2017-03-27,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
50535,SRR8134458,SRX4955494,SRS3996631,SRP167225,PRJNA501843,Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing,PRJNA501843,Other,Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf  also called shield stage  11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.,,,,,H24 3,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: PGC,H24 3,H24 3,smart2,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP167225,,,H24_3_R1.fastq H24_3_R2.fastq,fastq fastq,1303220750.0,5212883.0,H24 3 R1.fastq,0:125 1:125,A:353042196;C:298548859;G:299882991;T:351742904;N:3800,125,125,,,353042196,298548859,299882991,351742904,3800,SRX4955494,SRS3996631,SRA800727,"Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology","Shanghai Institute of Biochemistry and Cell Biology, CAS",2,0.95284,0.94903,0.03485,0.03522,0.8606,0.86168,0.49556,0.49795,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2019-02-01,Pharyngula,Embryo,Undetermined,Embryo Imprecise
50536,SRR8134459,SRX4955493,SRS3996630,SRP167225,PRJNA501843,Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing,PRJNA501843,Other,Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf  also called shield stage  11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.,,,,,H24 1,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: PGC,H24 1,H24 1,smart2,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP167225,,,H24_1_R1.fastq H24_1_R2.fastq,fastq fastq,1040367750.0,4161471.0,H24 1 R1.fastq,0:125 1:125,A:285190807;C:235796611;G:237165817;T:282211556;N:2959,125,125,,,285190807,235796611,237165817,282211556,2959,SRX4955493,SRS3996630,SRA800727,"Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology","Shanghai Institute of Biochemistry and Cell Biology, CAS",2,0.94648,0.94488,0.0507,0.05253,0.87353,0.87513,0.52936,0.52764,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2019-02-01,Pharyngula,Embryo,Undetermined,Embryo Imprecise
50537,SRR8134460,SRX4955492,SRS3996629,SRP167225,PRJNA501843,Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing,PRJNA501843,Other,Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf  also called shield stage  11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.,,,,,H24 2,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: PGC,H24 2,H24 2,smart2,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP167225,,,H24_2_R1.fastq H24_2_R2.fastq,fastq fastq,1003243000.0,4012972.0,H24 2 R1.fastq,0:125 1:125,A:275192369;C:227024454;G:228346661;T:272676506;N:3010,125,125,,,275192369,227024454,228346661,272676506,3010,SRX4955492,SRS3996629,SRA800727,"Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology","Shanghai Institute of Biochemistry and Cell Biology, CAS",2,0.94467,0.94348,0.06361,0.06541,0.8423,0.84478,0.51257,0.51745,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2019-02-01,Pharyngula,Embryo,Undetermined,Embryo Imprecise
50604,SRR8169175,SRX4989831,SRS4025849,SRP168005,PRJNA504385,Endothelial transcriptome of 1dpf Zebrafish empryo,PRJNA504385,Other,The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.,,,,Endothelial cells,EC,,strain:Tgfli1:EGFP  gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Endothelium|cell type:Endothelial|BioSampleModel:Model organism or animal,,,,,,,,,Endothelial cells,EC,EC,PolyA RNA Seq,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,,SRP168005,,,EC_R1.fastq EC_R2.fastq,fastq fastq,3373890496.0,22196648.0,EC R1.fastq,0:76 1:76,A:984631808;C:769706826;G:812424195;T:790813473;N:16314194,76,76,,,984631808,769706826,812424195,790813473,16314194,SRX4989831,SRS4025849,SRA805845,CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center,CSIR-Institute of Genomics and Integrative Biology,2,0.92323,0.92543,0.07989,0.0849,0.76842,0.77964,0.46181,0.47429,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2019-12-06,Pharyngula,Embryo,Endothelium,Cardiovascular System
50605,SRR8169176,SRX4989830,SRS4025850,SRP168005,PRJNA504385,Endothelial transcriptome of 1dpf Zebrafish empryo,PRJNA504385,Other,The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.,,,,Non endothelial cells,NEC,,strain:Tgfli1:EGFP  gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Whole organism devoid of endothelium|BioSampleModel:Model organism or animal,,,,,,,,,Non endothelial cells,NEC,NEC,PolyA RNA Seq,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,,SRP168005,,,NEC_R2.fastq NEC_R1.fastq,fastq fastq,3903685432.0,25682141.0,NEC R1.fastq,0:76 1:76,A:1078599801;C:913868400;G:942281029;T:950473482;N:18462720,76,76,,,1078599801,913868400,942281029,950473482,18462720,SRX4989830,SRS4025850,SRA805845,CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center,CSIR-Institute of Genomics and Integrative Biology,2,0.93037,0.92641,0.10373,0.11231,0.72644,0.74081,0.48329,0.48409,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,India,2019-12-06,Pharyngula,Embryo,Endothelium,Cardiovascular System
53427,SRR9854014,SRX6608456,SRS5172704,SRP216689,PRJNA557179,Role of the Exon Junction Complex in Danio rerio,GSE135019,Transcriptome Analysis,The exon  junction complex EJC is composed of three core proteins Rbm8a  Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq.  We find that  as in human cells  zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant  magoh mutant and wild type sibling embryos.  This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants,,,,RBM8A RIPSEQ Rep3,GSM3983830,,tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,RBM8A RIPSEQ Rep3,Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters  m 20   discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters  p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters  s  c  F 0.51  sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples,Whole embryo,None NA,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,All embryos were raised at 28.5C upto the required developmental timepoint.,developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,GSM3983830,GSM3983830: RBM8A RIPSEQ Rep3; Danio rerio; RIP Seq,GSM3983830,,1,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,GEO Accession:GSM3983830,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP216689,,loader:fastq load.py,ripseqB3.fastq.gz,fastq,1174462616.0,32753220.0,GSM3983830 r1,0:35.86,A:277856243;C:303697175;G:340240303;T:252574884;N:94011,35,,,,277856243,303697175,340240303,252574884,94011,SRX6608456,SRS5172704,SRA928193,GEO,"Guramrit Singh, Molecular Genetics, The Ohio State University",1,0.90426,,0.1746,,0.77341,,0.57553,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-07-29,Pharyngula,Embryo,Whole Organism,All anatomical structures
53428,SRR9854013,SRX6608455,SRS5172702,SRP216689,PRJNA557179,Role of the Exon Junction Complex in Danio rerio,GSE135019,Transcriptome Analysis,The exon  junction complex EJC is composed of three core proteins Rbm8a  Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq.  We find that  as in human cells  zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant  magoh mutant and wild type sibling embryos.  This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants,,,,RBM8A RIPSEQ Rep2,GSM3983829,,tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,RBM8A RIPSEQ Rep2,Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters  m 20   discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters  p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters  s  c  F 0.51  sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples,Whole embryo,None NA,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,All embryos were raised at 28.5C upto the required developmental timepoint.,developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,GSM3983829,GSM3983829: RBM8A RIPSEQ Rep2; Danio rerio; RIP Seq,GSM3983829,,1,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,GEO Accession:GSM3983829,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP216689,,loader:fastq load.py,ripseqB2.fastq.gz,fastq,65641776.0,2466295.0,GSM3983829 r1,0:26.62,A:18933213;C:16060113;G:13492679;T:17151951;N:3820,26,,,,18933213,16060113,13492679,17151951,3820,SRX6608455,SRS5172702,SRA928193,GEO,"Guramrit Singh, Molecular Genetics, The Ohio State University",1,0.17621,,0.02351,,0.88069,,0.60622,,15,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-07-29,Pharyngula,Embryo,Whole Organism,All anatomical structures
53429,SRR9854012,SRX6608454,SRS5172701,SRP216689,PRJNA557179,Role of the Exon Junction Complex in Danio rerio,GSE135019,Transcriptome Analysis,The exon  junction complex EJC is composed of three core proteins Rbm8a  Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq.  We find that  as in human cells  zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant  magoh mutant and wild type sibling embryos.  This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants,,,,RBM8A RIPSEQ Rep1,GSM3983828,,tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,RBM8A RIPSEQ Rep1,Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters  m 20   discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters  p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters  s  c  F 0.51  sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples,Whole embryo,None NA,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,All embryos were raised at 28.5C upto the required developmental timepoint.,developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,GSM3983828,GSM3983828: RBM8A RIPSEQ Rep1; Danio rerio; RIP Seq,GSM3983828,,1,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,GEO Accession:GSM3983828,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP216689,,loader:fastq load.py,ripseqB1.fastq.gz,fastq,403183413.0,11908151.0,GSM3983828 r1,0:33.86,A:80085450;C:111343041;G:140916198;T:70619085;N:219639,33,,,,80085450,111343041,140916198,70619085,219639,SRX6608454,SRS5172701,SRA928193,GEO,"Guramrit Singh, Molecular Genetics, The Ohio State University",1,0.862,,0.1026,,0.95359,,0.79372,,33,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-07-29,Pharyngula,Embryo,Whole Organism,All anatomical structures
55268,SRR10215484,SRX6935171,SRS5465204,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S06 Prim5,,strain:AB|dev stage:Prim 5|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,TeloPrime RNA seq Danio rerio  whole embryo  Prim 5  stage,Prim5 TeloPrime,Prim5 TeloPrime,TeloPrime Full Length cDNA amplification,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S06_Prim5_TeloPrime_1.fastq.gz S06_Prim5_TeloPrime_2.fastq.gz,fastq fastq,24558505000.0,122792525.0,S06 Prim5 TeloPrime 1.fastq.gz,0:100 1:100,A:6341287207;C:5749049203;G:5758305711;T:6709011836;N:851043,100,100,,,6341287207,5749049203,5758305711,6709011836,851043,SRX6935171,SRS5465204,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,2,0.85518,0.83013,0.01363,0.01378,0.80773,0.80992,0.38509,0.39167,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,other,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
56341,SRR10948891,SRX7615949,SRS6049208,SRP243873,PRJNA602610,Global promoter usage in the differentfractions of the cell during early zebrafish development,GSE144040,Other,We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome   Shield and Prim 5 stages of development.,,pubmed:33795334,,Prim5 Cyt CAGE,GSM4278497,,source name:24hpf stage embryo|tissue:zebrafish embryos|Stage:24hpf|fraction:Cytosolic|molecule type:capped RNAs,Prim5 Cyt CAGE,Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering  normalization  removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al.  2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format,24hpf stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|Stage:24hpf|fraction:Cytosolic|molecule type:capped RNAs,GSM4278497,GSM4278497: Prim5 Cyt CAGE; Danio rerio; OTHER,GSM4278497,,1,RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.,GEO Accession:GSM4278497,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP243873,,,Prim5_Cyt_L006_R1_001.fastq.gz Prim5_Cyt_L006_R2_001.fastq.gz,fastq fastq,11647548055.0,122605769.0,GSM4278497 r1,0:51 1:44,A:2440692679;C:3082646191;G:3382532043;T:2741423146;N:253996,51,44,,,2440692679,3082646191,3382532043,2741423146,253996,SRX7615949,SRS6049208,SRA1029879,GEO,"School of Biosciences, University of Birmingham",2,0.98284,0.34054,0.34811,0.12661,0.90753,0.95018,0.67956,0.71841,51,44,B,T,mate2 technical by mapping diff,illumina,hiseq_era,5prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2020-01-22,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
56342,SRR10948890,SRX7615948,SRS6049207,SRP243873,PRJNA602610,Global promoter usage in the differentfractions of the cell during early zebrafish development,GSE144040,Other,We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome   Shield and Prim 5 stages of development.,,pubmed:33795334,,Prim5 Nuc CAGE,GSM4278496,,source name:24hpf stage embryo|tissue:zebrafish embryos|Stage:24hpf|fraction:Nuclear|molecule type:capped RNAs,Prim5 Nuc CAGE,Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering  normalization  removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al.  2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format,24hpf stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|Stage:24hpf|fraction:Nuclear|molecule type:capped RNAs,GSM4278496,GSM4278496: Prim5 Nuc CAGE; Danio rerio; OTHER,GSM4278496,,1,RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.,GEO Accession:GSM4278496,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP243873,,,Prim5_Nuc_L006_R1_001.fastq.gz Prim5_Nuc_L006_R2_001.fastq.gz,fastq fastq,2052983345.0,21610351.0,GSM4278496 r1,0:51 1:44,A:448698187;C:513165511;G:563783876;T:527290561;N:45210,51,44,,,448698187,513165511,563783876,527290561,45210,SRX7615948,SRS6049207,SRA1029879,GEO,"School of Biosciences, University of Birmingham",2,0.95137,0.36483,0.38701,0.1658,0.82292,0.90638,0.65602,0.68468,51,44,B,T,mate2 technical by mapping diff,illumina,hiseq_era,5prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2020-01-22,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
66757,SRR23717090,SRX19578259,SRS16961241,SRP342737,PRJNA773778,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq],GSE186425,Other,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,DP1 36hpf,GSM7083138,,source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing,DP1 36hpf,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq,Zebrafish trunk region,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells|Stage:36 hpf,GSM7083138,GSM7083138: DP1 36hpf; Danio rerio; OTHER,GSM7083138 r1,GSM7083138,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342737,,,36hpf-DP1_FKDL202627688-1a_1.raw.fq.gz 36hpf-DP1_FKDL202627688-1a_2.raw.fq.gz,fastq fastq,36641999100.0,122139997.0,GSM7083138 r1,0:150 1:150,A:11840633171;C:5285812067;G:6638992204;T:12876249105;N:312553,150,150,,,11840633171,5285812067,6638992204,12876249105,312553,SRX19578259,SRS16961241,SRA1600575,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.8912,0.01571,0.09673,0.00653,0.86145,0.99849,0.61834,0.72033,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Trunk,Surface Structure
66758,SRR23717091,SRX19578258,SRS16961240,SRP342737,PRJNA773778,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq],GSE186425,Other,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,DP2 36hpf,GSM7083139,,source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing,DP2 36hpf,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq,Zebrafish trunk region,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells|Stage:36 hpf,GSM7083139,GSM7083139: DP2 36hpf; Danio rerio; OTHER,GSM7083139 r1,GSM7083139,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342737,,,36hpf-DP2_FKDL202627692-1a_1.raw.fq.gz 36hpf-DP2_FKDL202627692-1a_2.raw.fq.gz,fastq fastq,45339599100.0,151131997.0,GSM7083139 r1,0:150 1:150,A:14092451998;C:7125629842;G:9985822921;T:14135305628;N:388711,150,150,,,14092451998,7125629842,9985822921,14135305628,388711,SRX19578258,SRS16961240,SRA1600575,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.79702,0.00323,0.08737,0.00105,0.88663,0.99882,0.62618,0.6,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Trunk,Surface Structure
66759,SRR23717092,SRX19578257,SRS16961239,SRP342737,PRJNA773778,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq],GSE186425,Other,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,SP 36hpf,GSM7083140,,source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing,SP 36hpf,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq,Zebrafish trunk region,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells|Stage:36 hpf,GSM7083140,GSM7083140: SP 36hpf; Danio rerio; OTHER,GSM7083140 r1,GSM7083140,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342737,,,36hpf-SP_FKDL202627693-1a_1.raw.fq.gz 36hpf-SP_FKDL202627693-1a_2.raw.fq.gz,fastq fastq,44757872400.0,149192908.0,GSM7083140 r1,0:150 1:150,A:13194662551;C:6817138207;G:9879151250;T:14866177703;N:742689,150,150,,,13194662551,6817138207,9879151250,14866177703,742689,SRX19578257,SRS16961239,SRA1600575,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.7854,0.00221,0.062,0.00084,0.90995,0.99904,0.43661,0.67741,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Trunk,Surface Structure
69408,SRR18516951,SRX14648011,SRS12413418,SRP366502,PRJNA821148,CAGE seq total and nuclear RNA and nanT iCAGE acrosss 6 developmental stages,PRJNA821148,Other,In order to compare mRNA expression in the whole cell and the nucleus during development  we prepared CAGE seq libraries from total RNA as well as only from nuclear RNA as well as nanti CAGE on 6 developmental stages,,,,,DCD007418BS,,strain:AB|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|BioSampleModel:Model organism or animal,,,,,,,,,tagging CAGE Prim 5,DCD003639SQ,DCD003639SQ,tagging CAGE with Nuclear RNA  max read depth: 27,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP366502,,,CAGE-seq_Mueller_lab_0007AS.DCD003639SQ.USERirene.stevens.R1.fastq.gz,fastq,1328398677.0,49199951.0,CAGE seq Mueller lab 0007AS.DCD003639SQ.USERirene.stevens.R1.fastq.gz,0:27 1:0,A:347247893;C:293260323;G:377992379;T:309837948;N:60134,27,0,,,347247893,293260323,377992379,309837948,60134,SRX14648011,SRS12413418,SRA1393751,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.46699,,0.13006,,0.78332,,0.8225,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures