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120 rows where devstage_curation = "Hatching" and experiment.library_selection = "other"

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tissue_curation 4

technology 3

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

experiment.platform 1

experiment.library_selection 1

  • other · 120 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Hatching · 120 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
79 79 DRR032745 DRX029551 DRS049950 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr 60h 2 SAMD00028142   sample name:Dr 60h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028142 DRX029551 Dr 60h 2 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028142       3875337000.0 38753370.0 DRR032745 0:100 1:0 A:1042558903;C:899892111;G:896867583;T:1035981420;N:36983 100 0     1042558903 899892111 896867583 1035981420 36983 DRX029551 DRS049950 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.91891   0.09445   0.66156   0.45564   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Hatching Embryo Whole Organism All anatomical structures
80 80 DRR032744 DRX029550 DRS049949 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr 60h 1 SAMD00028141   sample name:Dr 60h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028141 DRX029550 Dr 60h 1 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028141       3538468200.0 35384682.0 DRR032744 0:100 1:0 A:960664313;C:812459988;G:809014008;T:956295205;N:34686 100 0     960664313 812459988 809014008 956295205 34686 DRX029550 DRS049949 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.91388   0.10346   0.66076   0.45203   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Hatching Embryo Whole Organism All anatomical structures
84 84 DRR032740 DRX029546 DRS049945 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr 48h 2 SAMD00028137   sample name:Dr 48h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028137 DRX029546 Dr 48h 2 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028137       3702804700.0 37028047.0 DRR032740 0:100 1:0 A:993931475;C:862403562;G:857808891;T:988623734;N:37038 100 0     993931475 862403562 857808891 988623734 37038 DRX029546 DRS049945 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92508   0.08526   0.68349   0.45769   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Hatching Embryo Whole Organism All anatomical structures
85 85 DRR032739 DRX029545 DRS049944 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 50 individuals Dr 48h 1 SAMD00028136   sample name:Dr 48h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028136 DRX029545 Dr 48h 1 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028136       3980240400.0 39802404.0 DRR032739 0:100 1:0 A:1070497788;C:925240883;G:920038728;T:1064422474;N:40527 100 0     1070497788 925240883 920038728 1064422474 40527 DRX029545 DRS049944 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.92349   0.08681   0.67874   0.46565   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Hatching Embryo Whole Organism All anatomical structures
7946 7946 ERR015563 ERX005934 ERS012707 ERP000263 PRJEB2208 Zebrafish gene three prime end pull down for genome annotation E-MTAB-308 Transcriptome Analysis         E MTAB 308:Zebrafish embryo 2 dpf 2 SAMEA898403 Wellcome Sanger Institute Age:2 days|Alias:E MTAB 308:Zebrafish embryo 2 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:ERS012707|Sample Name:ERS012707|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 2 dpf three prime pull down paired end 250 to 300 bp insert Zebrafish embro 2 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:2 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_2.srf srf 990308120.0 6515185.0 E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 2 dpf three prime pull down paired end 250 to 300 bp insert 0:76 1:76 A:279665076;C:200433201;G:189692111;T:304366697;N:16151035 76 76     279665076 200433201 189692111 304366697 16151035 ERX005934 ERS012707 ERA010603 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.93964 0.94008 0.40095 0.39969 0.74424 0.74915 0.49535 0.49761 76 76 B B biological fallback assumption illumina early_illumina 3prime other unknown bulk unknown unknown   United Kingdom 2010-08-19 Hatching Embryo Whole Organism All anatomical structures
33886 33886 SRR30907854 SRX26311176 SRS22839346 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish E2 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:9|BioSampleModel:Model organism or animal                 zebrafish 9 9 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241016_E2.R1.raw.fastq.gz L1EFA241016_E2.R2.raw.fastq.gz fastq fastq 8244899282.0 27300991.0 L1EFA241016 E2.R1.raw.fastq.gz 0:151 1:151 A:2186915781;C:1920264424;G:1996130250;T:2141502974;N:85853 151 151     2186915781 1920264424 1996130250 2141502974 85853 SRX26311176 SRS22839346 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33887 33887 SRR30907855 SRX26311175 SRS22839344 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish E1 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:7|BioSampleModel:Model organism or animal                 zebrafish 7 7 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241015_E1.R1.raw.fastq.gz L1EFA241015_E1.R2.raw.fastq.gz fastq fastq 7083661566.0 23455833.0 L1EFA241015 E1.R1.raw.fastq.gz 0:151 1:151 A:1848193884;C:1679679234;G:1751186922;T:1804529897;N:71629 151 151     1848193884 1679679234 1751186922 1804529897 71629 SRX26311175 SRS22839344 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33888 33888 SRR30907856 SRX26311174 SRS22839345 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish A3 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:5|BioSampleModel:Model organism or animal                 zebrafish 5 5 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241014_A3.R1.raw.fastq.gz L1EFA241014_A3.R2.raw.fastq.gz fastq fastq 7926170898.0 26245599.0 L1EFA241014 A3.R1.raw.fastq.gz 0:151 1:151 A:2128209130;C:1819597773;G:1900902610;T:2077378388;N:82997 151 151     2128209130 1819597773 1900902610 2077378388 82997 SRX26311174 SRS22839345 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33889 33889 SRR30907857 SRX26311173 SRS22839343 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish A2 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:3|BioSampleModel:Model organism or animal                 zebrafish 3 3 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241013_A2.R1.raw.fastq.gz L1EFA241013_A2.R2.raw.fastq.gz fastq fastq 7889851774.0 26125337.0 L1EFA241013 A2.R1.raw.fastq.gz 0:151 1:151 A:2121620438;C:1812268472;G:1879664190;T:2076216345;N:82329 151 151     2121620438 1812268472 1879664190 2076216345 82329 SRX26311173 SRS22839343 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33890 33890 SRR30907858 SRX26311172 SRS22839342 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish E3 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:11|BioSampleModel:Model organism or animal                 zebrafish 11 11 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241017_E3.R1.raw.fastq.gz L1EFA241017_E3.R2.raw.fastq.gz fastq fastq 7824546992.0 25909096.0 L1EFA241017 E3.R1.raw.fastq.gz 0:151 1:151 A:2082463940;C:1810596613;G:1891675714;T:2039730477;N:80248 151 151     2082463940 1810596613 1891675714 2039730477 80248 SRX26311172 SRS22839342 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33891 33891 SRR30907859 SRX26311171 SRS22839341 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish A1 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:1|BioSampleModel:Model organism or animal                 zebrafish 1 1 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241012_A1.R1.raw.fastq.gz L1EFA241012_A1.R2.raw.fastq.gz fastq fastq 8017250474.0 26547187.0 L1EFA241012 A1.R1.raw.fastq.gz 0:151 1:151 A:2139416119;C:1853218216;G:1930287523;T:2094246996;N:81620 151 151     2139416119 1853218216 1930287523 2094246996 81620 SRX26311171 SRS22839341 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33990 33990 SRR31030860 SRX26416598 SRS22936450 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES GAPDH Rep4 minus GSM8578751   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing ZF NES GAPDH Rep4 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578751 GSM8578751: ZF NES GAPDH Rep4 minus; Danio rerio; OTHER GSM8578751 r1 GSM8578751 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_GAPDH_Rep4_minus.R1.fq.gz ZF_NES_GAPDH_Rep4_minus.R2.fq.gz fastq fastq 1100578200.0 3668594.0 GSM8578751 r1 0:150 1:150 A:287878221;C:249390946;G:265835736;T:297454600;N:18697 150 150     287878221 249390946 265835736 297454600 18697 SRX26416598 SRS22936450 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33991 33991 SRR31030861 SRX26416597 SRS22936451 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES GAPDH Rep3 plus GSM8578750   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing ZF NES GAPDH Rep3 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578750 GSM8578750: ZF NES GAPDH Rep3 plus; Danio rerio; OTHER GSM8578750 r1 GSM8578750 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_GAPDH_Rep3_plus.R1.fq.gz ZF_NES_GAPDH_Rep3_plus.R2.fq.gz fastq fastq 1231779300.0 4105931.0 GSM8578750 r1 0:150 1:150 A:322256597;C:278991471;G:297394980;T:333116282;N:19970 150 150     322256597 278991471 297394980 333116282 19970 SRX26416597 SRS22936451 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33992 33992 SRR31030862 SRX26416596 SRS22936449 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES GAPDH Rep3 minus GSM8578749   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing ZF NES GAPDH Rep3 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578749 GSM8578749: ZF NES GAPDH Rep3 minus; Danio rerio; OTHER GSM8578749 r1 GSM8578749 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_GAPDH_Rep3_minus.R1.fq.gz ZF_NES_GAPDH_Rep3_minus.R2.fq.gz fastq fastq 1002124500.0 3340415.0 GSM8578749 r1 0:150 1:150 A:262024969;C:227163761;G:242157218;T:270761424;N:17128 150 150     262024969 227163761 242157218 270761424 17128 SRX26416596 SRS22936449 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33993 33993 SRR31030863 SRX26416595 SRS22936448 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES GAPDH Rep2 plus GSM8578748   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing ZF NES GAPDH Rep2 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578748 GSM8578748: ZF NES GAPDH Rep2 plus; Danio rerio; OTHER GSM8578748 r1 GSM8578748 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_GAPDH_Rep2_plus.R1.fq.gz ZF_NES_GAPDH_Rep2_plus.R2.fq.gz fastq fastq 1051565100.0 3505217.0 GSM8578748 r1 0:150 1:150 A:275784945;C:237523425;G:253300749;T:284937948;N:18033 150 150     275784945 237523425 253300749 284937948 18033 SRX26416595 SRS22936448 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33994 33994 SRR31030864 SRX26416594 SRS22936447 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES GAPDH Rep2 minus GSM8578747   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing ZF NES GAPDH Rep2 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578747 GSM8578747: ZF NES GAPDH Rep2 minus; Danio rerio; OTHER GSM8578747 r1 GSM8578747 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_GAPDH_Rep2_minus.R1.fq.gz ZF_NES_GAPDH_Rep2_minus.R2.fq.gz fastq fastq 1021837200.0 3406124.0 GSM8578747 r1 0:150 1:150 A:268290250;C:230525208;G:245949056;T:277056045;N:16641 150 150     268290250 230525208 245949056 277056045 16641 SRX26416594 SRS22936447 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33995 33995 SRR31030865 SRX26416593 SRS22936446 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES GAPDH Rep1 plus GSM8578746   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing ZF NES GAPDH Rep1 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578746 GSM8578746: ZF NES GAPDH Rep1 plus; Danio rerio; OTHER GSM8578746 r1 GSM8578746 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_GAPDH_Rep1_plus.R1.fq.gz ZF_NES_GAPDH_Rep1_plus.R2.fq.gz fastq fastq 1093620300.0 3645401.0 GSM8578746 r1 0:150 1:150 A:285989719;C:247805250;G:264181043;T:295625946;N:18342 150 150     285989719 247805250 264181043 295625946 18342 SRX26416593 SRS22936446 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33996 33996 SRR31030866 SRX26416592 SRS22936445 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES GAPDH Rep1 minus GSM8578745   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing ZF NES GAPDH Rep1 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578745 GSM8578745: ZF NES GAPDH Rep1 minus; Danio rerio; OTHER GSM8578745 r1 GSM8578745 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_GAPDH_Rep1_minus.R1.fq.gz ZF_NES_GAPDH_Rep1_minus.R2.fq.gz fastq fastq 911747100.0 3039157.0 GSM8578745 r1 0:150 1:150 A:239833349;C:205185786;G:218897710;T:247814511;N:15744 150 150     239833349 205185786 218897710 247814511 15744 SRX26416592 SRS22936445 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33997 33997 SRR31030867 SRX26416591 SRS22936444 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B MALAT1 Rep4 plus GSM8578744   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing ZF H2B MALAT1 Rep4 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF GSM8578744 GSM8578744: ZF H2B MALAT1 Rep4 plus; Danio rerio; OTHER GSM8578744 r1 GSM8578744 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_MALAT1_Rep4_plus.R1.fq.gz ZF_H2B_MALAT1_Rep4_plus.R2.fq.gz fastq fastq 842103300.0 2807011.0 GSM8578744 r1 0:150 1:150 A:204870477;C:222752099;G:215404135;T:199062275;N:14314 150 150     204870477 222752099 215404135 199062275 14314 SRX26416591 SRS22936444 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33998 33998 SRR31030868 SRX26416590 SRS22936442 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B MALAT1 Rep4 minus GSM8578743   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing ZF H2B MALAT1 Rep4 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF GSM8578743 GSM8578743: ZF H2B MALAT1 Rep4 minus; Danio rerio; OTHER GSM8578743 r1 GSM8578743 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_MALAT1_Rep4_minus.R1.fq.gz ZF_H2B_MALAT1_Rep4_minus.R2.fq.gz fastq fastq 1166375100.0 3887917.0 GSM8578743 r1 0:150 1:150 A:283781955;C:308660466;G:298298204;T:275614377;N:20098 150 150     283781955 308660466 298298204 275614377 20098 SRX26416590 SRS22936442 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
33999 33999 SRR31030869 SRX26416589 SRS22936443 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B MALAT1 Rep3 plus GSM8578742   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing ZF H2B MALAT1 Rep3 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF GSM8578742 GSM8578742: ZF H2B MALAT1 Rep3 plus; Danio rerio; OTHER GSM8578742 r1 GSM8578742 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_MALAT1_Rep3_plus.R1.fq.gz ZF_H2B_MALAT1_Rep3_plus.R2.fq.gz fastq fastq 1159439400.0 3864798.0 GSM8578742 r1 0:150 1:150 A:282055391;C:306842216;G:296569227;T:273952570;N:19996 150 150     282055391 306842216 296569227 273952570 19996 SRX26416589 SRS22936443 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34000 34000 SRR31030870 SRX26416588 SRS22936440 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B MALAT1 Rep3 minus GSM8578741   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing ZF H2B MALAT1 Rep3 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF GSM8578741 GSM8578741: ZF H2B MALAT1 Rep3 minus; Danio rerio; OTHER GSM8578741 r1 GSM8578741 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_MALAT1_Rep3_minus.R1.fq.gz ZF_H2B_MALAT1_Rep3_minus.R2.fq.gz fastq fastq 1008297600.0 3360992.0 GSM8578741 r1 0:150 1:150 A:245277585;C:266840408;G:257911846;T:238251305;N:16456 150 150     245277585 266840408 257911846 238251305 16456 SRX26416588 SRS22936440 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34001 34001 SRR31030871 SRX26416587 SRS22936441 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B MALAT1 Rep2 plus GSM8578740   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing ZF H2B MALAT1 Rep2 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF GSM8578740 GSM8578740: ZF H2B MALAT1 Rep2 plus; Danio rerio; OTHER GSM8578740 r1 GSM8578740 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_MALAT1_Rep2_plus.R1.fq.gz ZF_H2B_MALAT1_Rep2_plus.R2.fq.gz fastq fastq 1419263400.0 4730878.0 GSM8578740 r1 0:150 1:150 A:345302268;C:375591885;G:362956395;T:335387828;N:25024 150 150     345302268 375591885 362956395 335387828 25024 SRX26416587 SRS22936441 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34002 34002 SRR31030872 SRX26416586 SRS22936439 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B MALAT1 Rep2 minus GSM8578739   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing ZF H2B MALAT1 Rep2 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF GSM8578739 GSM8578739: ZF H2B MALAT1 Rep2 minus; Danio rerio; OTHER GSM8578739 r1 GSM8578739 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_MALAT1_Rep2_minus.R1.fq.gz ZF_H2B_MALAT1_Rep2_minus.R2.fq.gz fastq fastq 1249910700.0 4166369.0 GSM8578739 r1 0:150 1:150 A:304074828;C:330741431;G:319677748;T:295395235;N:21458 150 150     304074828 330741431 319677748 295395235 21458 SRX26416586 SRS22936439 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34003 34003 SRR31030873 SRX26416585 SRS22936438 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B MALAT1 Rep1 plus GSM8578738   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing ZF H2B MALAT1 Rep1 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF GSM8578738 GSM8578738: ZF H2B MALAT1 Rep1 plus; Danio rerio; OTHER GSM8578738 r1 GSM8578738 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_MALAT1_Rep1_plus.R1.fq.gz ZF_H2B_MALAT1_Rep1_plus.R2.fq.gz fastq fastq 1257872700.0 4192909.0 GSM8578738 r1 0:150 1:150 A:306022947;C:332851039;G:321699513;T:297277788;N:21413 150 150     306022947 332851039 321699513 297277788 21413 SRX26416585 SRS22936438 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34004 34004 SRR31030874 SRX26416584 SRS22936437 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B MALAT1 Rep1 minus GSM8578737   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing ZF H2B MALAT1 Rep1 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF GSM8578737 GSM8578737: ZF H2B MALAT1 Rep1 minus; Danio rerio; OTHER GSM8578737 r1 GSM8578737 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_MALAT1_Rep1_minus.R1.fq.gz ZF_H2B_MALAT1_Rep1_minus.R2.fq.gz fastq fastq 1377040200.0 4590134.0 GSM8578737 r1 0:150 1:150 A:335021330;C:364359707;G:352178356;T:325457746;N:23061 150 150     335021330 364359707 352178356 325457746 23061 SRX26416584 SRS22936437 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34005 34005 SRR31030875 SRX26416583 SRS22936435 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B GAPDH Rep4 plus GSM8578736   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing ZF H2B GAPDH Rep4 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF GSM8578736 GSM8578736: ZF H2B GAPDH Rep4 plus; Danio rerio; OTHER GSM8578736 r1 GSM8578736 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_GAPDH_Rep4_plus.R1.fq.gz ZF_H2B_GAPDH_Rep4_plus.R2.fq.gz fastq fastq 1051103100.0 3503677.0 GSM8578736 r1 0:150 1:150 A:274220771;C:238733668;G:254670769;T:283460283;N:17609 150 150     274220771 238733668 254670769 283460283 17609 SRX26416583 SRS22936435 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate1-mate2 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34006 34006 SRR31030876 SRX26416582 SRS22936436 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B GAPDH Rep4 minus GSM8578735   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing ZF H2B GAPDH Rep4 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF GSM8578735 GSM8578735: ZF H2B GAPDH Rep4 minus; Danio rerio; OTHER GSM8578735 r1 GSM8578735 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_GAPDH_Rep4_minus.R1.fq.gz ZF_H2B_GAPDH_Rep4_minus.R2.fq.gz fastq fastq 1206485700.0 4021619.0 GSM8578735 r1 0:150 1:150 A:314740194;C:274101014;G:292357972;T:325267132;N:19388 150 150     314740194 274101014 292357972 325267132 19388 SRX26416582 SRS22936436 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate1-mate2 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34007 34007 SRR31030877 SRX26416581 SRS22936434 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B GAPDH Rep3 plus GSM8578734   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing ZF H2B GAPDH Rep3 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF GSM8578734 GSM8578734: ZF H2B GAPDH Rep3 plus; Danio rerio; OTHER GSM8578734 r1 GSM8578734 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_GAPDH_Rep3_plus.R1.fq.gz ZF_H2B_GAPDH_Rep3_plus.R2.fq.gz fastq fastq 1140550200.0 3801834.0 GSM8578734 r1 0:150 1:150 A:297636297;C:258828826;G:276373993;T:307692213;N:18871 150 150     297636297 258828826 276373993 307692213 18871 SRX26416581 SRS22936434 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate1-mate2 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34008 34008 SRR31030878 SRX26416580 SRS22936433 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B GAPDH Rep3 minus GSM8578733   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing ZF H2B GAPDH Rep3 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF GSM8578733 GSM8578733: ZF H2B GAPDH Rep3 minus; Danio rerio; OTHER GSM8578733 r1 GSM8578733 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_GAPDH_Rep3_minus.R1.fq.gz ZF_H2B_GAPDH_Rep3_minus.R2.fq.gz fastq fastq 782406600.0 2608022.0 GSM8578733 r1 0:150 1:150 A:204132316;C:177696721;G:189675433;T:210888939;N:13191 150 150     204132316 177696721 189675433 210888939 13191 SRX26416580 SRS22936433 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate1-mate2 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34009 34009 SRR31030879 SRX26416579 SRS22936431 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B GAPDH Rep2 plus GSM8578732   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing ZF H2B GAPDH Rep2 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF GSM8578732 GSM8578732: ZF H2B GAPDH Rep2 plus; Danio rerio; OTHER GSM8578732 r1 GSM8578732 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_GAPDH_Rep2_plus.R1.fq.gz ZF_H2B_GAPDH_Rep2_plus.R2.fq.gz fastq fastq 958297200.0 3194324.0 GSM8578732 r1 0:150 1:150 A:250011335;C:217600823;G:232206339;T:258462392;N:16311 150 150     250011335 217600823 232206339 258462392 16311 SRX26416579 SRS22936431 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate1-mate2 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34010 34010 SRR31030880 SRX26416578 SRS22936432 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B GAPDH Rep2 minus GSM8578731   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing ZF H2B GAPDH Rep2 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF GSM8578731 GSM8578731: ZF H2B GAPDH Rep2 minus; Danio rerio; OTHER GSM8578731 r1 GSM8578731 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_GAPDH_Rep2_minus.R1.fq.gz ZF_H2B_GAPDH_Rep2_minus.R2.fq.gz fastq fastq 1020926700.0 3403089.0 GSM8578731 r1 0:150 1:150 A:266429488;C:231749424;G:247353147;T:275377720;N:16921 150 150     266429488 231749424 247353147 275377720 16921 SRX26416578 SRS22936432 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate1-mate2 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34011 34011 SRR31030881 SRX26416577 SRS22936430 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B GAPDH Rep1 plus GSM8578730   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing ZF H2B GAPDH Rep1 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF GSM8578730 GSM8578730: ZF H2B GAPDH Rep1 plus; Danio rerio; OTHER GSM8578730 r1 GSM8578730 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_GAPDH_Rep1_plus.R1.fq.gz ZF_H2B_GAPDH_Rep1_plus.R2.fq.gz fastq fastq 1134318600.0 3781062.0 GSM8578730 r1 0:150 1:150 A:295931335;C:257596481;G:274848790;T:305922827;N:19167 150 150     295931335 257596481 274848790 305922827 19167 SRX26416577 SRS22936430 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate1-mate2 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34012 34012 SRR31030882 SRX26416576 SRS22936429 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF H2B GAPDH Rep1 minus GSM8578729   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing ZF H2B GAPDH Rep1 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF GSM8578729 GSM8578729: ZF H2B GAPDH Rep1 minus; Danio rerio; OTHER GSM8578729 r1 GSM8578729 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_H2B_GAPDH_Rep1_minus.R1.fq.gz ZF_H2B_GAPDH_Rep1_minus.R2.fq.gz fastq fastq 752638800.0 2508796.0 GSM8578729 r1 0:150 1:150 A:196331185;C:170899863;G:182460258;T:202935049;N:12445 150 150     196331185 170899863 182460258 202935049 12445 SRX26416576 SRS22936429 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate1-mate2 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34013 34013 SRR31031004 SRX26416454 SRS22936307 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb WT pDBF Rep3 GSM8578770   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF|geo loc name:missing|collection date:missing Zeb WT pDBF Rep3 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF GSM8578770 GSM8578770: Zeb WT pDBF Rep3; Danio rerio; OTHER GSM8578770 r1 GSM8578770 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_WT_pDBF_Rep3.R1.fq.gz Zeb_WT_pDBF_Rep3.R2.fq.gz fastq fastq 23216831100.0 77389437.0 GSM8578770 r1 0:150 1:150 A:7577896837;C:3508911439;G:4823311862;T:7306393244;N:317718 150 150     7577896837 3508911439 4823311862 7306393244 317718 SRX26416454 SRS22936307 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34014 34014 SRR31031005 SRX26416453 SRS22936305 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb WT pDBF Rep2 GSM8578769   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF|geo loc name:missing|collection date:missing Zeb WT pDBF Rep2 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF GSM8578769 GSM8578769: Zeb WT pDBF Rep2; Danio rerio; OTHER GSM8578769 r1 GSM8578769 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_WT_pDBF_Rep2.R1.fq.gz Zeb_WT_pDBF_Rep2.R2.fq.gz fastq fastq 27237049500.0 90790165.0 GSM8578769 r1 0:150 1:150 A:8800724632;C:4062692793;G:5651432074;T:8721823175;N:376826 150 150     8800724632 4062692793 5651432074 8721823175 376826 SRX26416453 SRS22936305 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34015 34015 SRR31031006 SRX26416452 SRS22936306 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb WT pDBF Rep1 GSM8578768   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF|geo loc name:missing|collection date:missing Zeb WT pDBF Rep1 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF GSM8578768 GSM8578768: Zeb WT pDBF Rep1; Danio rerio; OTHER GSM8578768 r1 GSM8578768 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_WT_pDBF_Rep1.R1.fq.gz Zeb_WT_pDBF_Rep1.R2.fq.gz fastq fastq 22364115300.0 74547051.0 GSM8578768 r1 0:150 1:150 A:7336106577;C:3346831944;G:4451536371;T:7229335436;N:304972 150 150     7336106577 3346831944 4451536371 7229335436 304972 SRX26416452 SRS22936306 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34016 34016 SRR31031007 SRX26416451 SRS22936304 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb WT mDBF Rep3 GSM8578767   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF|geo loc name:missing|collection date:missing Zeb WT mDBF Rep3 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF GSM8578767 GSM8578767: Zeb WT mDBF Rep3; Danio rerio; OTHER GSM8578767 r1 GSM8578767 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_WT_mDBF_Rep3.R1.fq.gz Zeb_WT_mDBF_Rep3.R2.fq.gz fastq fastq 20112719100.0 67042397.0 GSM8578767 r1 0:150 1:150 A:6537370232;C:2924919118;G:3973928235;T:6676228153;N:273362 150 150     6537370232 2924919118 3973928235 6676228153 273362 SRX26416451 SRS22936304 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34017 34017 SRR31031008 SRX26416450 SRS22936303 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb WT mDBF Rep2 GSM8578766   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF|geo loc name:missing|collection date:missing Zeb WT mDBF Rep2 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF GSM8578766 GSM8578766: Zeb WT mDBF Rep2; Danio rerio; OTHER GSM8578766 r1 GSM8578766 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_WT_mDBF_Rep2.R1.fq.gz Zeb_WT_mDBF_Rep2.R2.fq.gz fastq fastq 24839552100.0 82798507.0 GSM8578766 r1 0:150 1:150 A:8176074473;C:3715794630;G:4984816273;T:7962528150;N:338574 150 150     8176074473 3715794630 4984816273 7962528150 338574 SRX26416450 SRS22936303 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34018 34018 SRR31031009 SRX26416449 SRS22936302 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb WT mDBF Rep1 GSM8578765   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF|geo loc name:missing|collection date:missing Zeb WT mDBF Rep1 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF GSM8578765 GSM8578765: Zeb WT mDBF Rep1; Danio rerio; OTHER GSM8578765 r1 GSM8578765 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_WT_mDBF_Rep1.R1.fq.gz Zeb_WT_mDBF_Rep1.R2.fq.gz fastq fastq 23029785600.0 76765952.0 GSM8578765 r1 0:150 1:150 A:7509388471;C:3438475939;G:4820328116;T:7261277960;N:315114 150 150     7509388471 3438475939 4820328116 7261277960 315114 SRX26416449 SRS22936302 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34019 34019 SRR31031010 SRX26416448 SRS22936301 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb NES pDBF Rep2 GSM8578764   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing Zeb NES pDBF Rep2 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578764 GSM8578764: Zeb NES pDBF Rep2; Danio rerio; OTHER GSM8578764 r1 GSM8578764 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_NES_pDBF_Rep2.R1.fq.gz Zeb_NES_pDBF_Rep2.R2.fq.gz fastq fastq 25465584900.0 84885283.0 GSM8578764 r1 0:150 1:150 A:7944190976;C:4330095891;G:5473069331;T:7718120992;N:107710 150 150     7944190976 4330095891 5473069331 7718120992 107710 SRX26416448 SRS22936301 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34020 34020 SRR31031011 SRX26416447 SRS22936300 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb NES pDBF Rep1 GSM8578763   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing Zeb NES pDBF Rep1 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578763 GSM8578763: Zeb NES pDBF Rep1; Danio rerio; OTHER GSM8578763 r1 GSM8578763 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_NES_pDBF_Rep1.R1.fq.gz Zeb_NES_pDBF_Rep1.R2.fq.gz fastq fastq 21107351400.0 70357838.0 GSM8578763 r1 0:150 1:150 A:6528579219;C:3620666961;G:4496642830;T:6461373643;N:88747 150 150     6528579219 3620666961 4496642830 6461373643 88747 SRX26416447 SRS22936300 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34021 34021 SRR31031012 SRX26416446 SRS22936299 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb NES mDBF Rep2 GSM8578762   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing Zeb NES mDBF Rep2 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578762 GSM8578762: Zeb NES mDBF Rep2; Danio rerio; OTHER GSM8578762 r1 GSM8578762 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_NES_mDBF_Rep2.R1.fq.gz Zeb_NES_mDBF_Rep2.R2.fq.gz fastq fastq 21542967300.0 71809891.0 GSM8578762 r1 0:150 1:150 A:6722613760;C:3654507931;G:4628076548;T:6537678084;N:90977 150 150     6722613760 3654507931 4628076548 6537678084 90977 SRX26416446 SRS22936299 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34022 34022 SRR31031013 SRX26416445 SRS22936297 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   Zeb NES mDBF Rep1 GSM8578761   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing Zeb NES mDBF Rep1 OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578761 GSM8578761: Zeb NES mDBF Rep1; Danio rerio; OTHER GSM8578761 r1 GSM8578761 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     Zeb_NES_mDBF_Rep1.R1.fq.gz Zeb_NES_mDBF_Rep1.R2.fq.gz fastq fastq 23038870800.0 76796236.0 GSM8578761 r1 0:150 1:150 A:7216059153;C:3815899397;G:4909028200;T:7097787584;N:96466 150 150     7216059153 3815899397 4909028200 7097787584 96466 SRX26416445 SRS22936297 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B mate2-mate1 similar by mapping diff illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34023 34023 SRR31031014 SRX26416444 SRS22936298 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES MALAT1 Rep4 plus GSM8578760   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing ZF NES MALAT1 Rep4 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578760 GSM8578760: ZF NES MALAT1 Rep4 plus; Danio rerio; OTHER GSM8578760 r1 GSM8578760 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_MALAT1_Rep4_plus.R1.fq.gz ZF_NES_MALAT1_Rep4_plus.R2.fq.gz fastq fastq 1091293200.0 3637644.0 GSM8578760 r1 0:150 1:150 A:265519561;C:288647650;G:279105515;T:258001510;N:18964 150 150     265519561 288647650 279105515 258001510 18964 SRX26416444 SRS22936298 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34024 34024 SRR31031015 SRX26416443 SRS22936296 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES MALAT1 Rep4 minus GSM8578759   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing ZF NES MALAT1 Rep4 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578759 GSM8578759: ZF NES MALAT1 Rep4 minus; Danio rerio; OTHER GSM8578759 r1 GSM8578759 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_MALAT1_Rep4_minus.R1.fq.gz ZF_NES_MALAT1_Rep4_minus.R2.fq.gz fastq fastq 1395963600.0 4653212.0 GSM8578759 r1 0:150 1:150 A:339654289;C:369433701;G:356957685;T:329893853;N:24072 150 150     339654289 369433701 356957685 329893853 24072 SRX26416443 SRS22936296 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34025 34025 SRR31031016 SRX26416442 SRS22936295 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES MALAT1 Rep3 plus GSM8578758   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing ZF NES MALAT1 Rep3 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578758 GSM8578758: ZF NES MALAT1 Rep3 plus; Danio rerio; OTHER GSM8578758 r1 GSM8578758 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_MALAT1_Rep3_plus.R1.fq.gz ZF_NES_MALAT1_Rep3_plus.R2.fq.gz fastq fastq 1556195100.0 5187317.0 GSM8578758 r1 0:150 1:150 A:378553535;C:411730281;G:398086882;T:367797563;N:26839 150 150     378553535 411730281 398086882 367797563 26839 SRX26416442 SRS22936295 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34026 34026 SRR31031017 SRX26416441 SRS22936294 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES MALAT1 Rep3 minus GSM8578757   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing ZF NES MALAT1 Rep3 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578757 GSM8578757: ZF NES MALAT1 Rep3 minus; Danio rerio; OTHER GSM8578757 r1 GSM8578757 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_MALAT1_Rep3_minus.R1.fq.gz ZF_NES_MALAT1_Rep3_minus.R2.fq.gz fastq fastq 1511328900.0 5037763.0 GSM8578757 r1 0:150 1:150 A:367639521;C:400036694;G:386523395;T:357103340;N:25950 150 150     367639521 400036694 386523395 357103340 25950 SRX26416441 SRS22936294 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34027 34027 SRR31031018 SRX26416440 SRS22936293 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES MALAT1 Rep2 plus GSM8578756   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing ZF NES MALAT1 Rep2 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578756 GSM8578756: ZF NES MALAT1 Rep2 plus; Danio rerio; OTHER GSM8578756 r1 GSM8578756 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_MALAT1_Rep2_plus.R1.fq.gz ZF_NES_MALAT1_Rep2_plus.R2.fq.gz fastq fastq 1451137800.0 4837126.0 GSM8578756 r1 0:150 1:150 A:353052445;C:383981771;G:371154128;T:342925275;N:24181 150 150     353052445 383981771 371154128 342925275 24181 SRX26416440 SRS22936293 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34028 34028 SRR31031019 SRX26416439 SRS22936292 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES MALAT1 Rep2 minus GSM8578755   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing ZF NES MALAT1 Rep2 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578755 GSM8578755: ZF NES MALAT1 Rep2 minus; Danio rerio; OTHER GSM8578755 r1 GSM8578755 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_MALAT1_Rep2_minus.R1.fq.gz ZF_NES_MALAT1_Rep2_minus.R2.fq.gz fastq fastq 1286489400.0 4288298.0 GSM8578755 r1 0:150 1:150 A:312986127;C:340482608;G:329001591;T:303997982;N:21092 150 150     312986127 340482608 329001591 303997982 21092 SRX26416439 SRS22936292 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34029 34029 SRR31031020 SRX26416438 SRS22936291 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES MALAT1 Rep1 plus GSM8578754   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing ZF NES MALAT1 Rep1 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578754 GSM8578754: ZF NES MALAT1 Rep1 plus; Danio rerio; OTHER GSM8578754 r1 GSM8578754 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_MALAT1_Rep1_plus.R1.fq.gz ZF_NES_MALAT1_Rep1_plus.R2.fq.gz fastq fastq 1146380100.0 3821267.0 GSM8578754 r1 0:150 1:150 A:278826422;C:303464534;G:293239572;T:270830265;N:19307 150 150     278826422 303464534 293239572 270830265 19307 SRX26416438 SRS22936291 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34030 34030 SRR31031021 SRX26416437 SRS22936289 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES MALAT1 Rep1 minus GSM8578753   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing ZF NES MALAT1 Rep1 minus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF GSM8578753 GSM8578753: ZF NES MALAT1 Rep1 minus; Danio rerio; OTHER GSM8578753 r1 GSM8578753 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_MALAT1_Rep1_minus.R1.fq.gz ZF_NES_MALAT1_Rep1_minus.R2.fq.gz fastq fastq 1149087000.0 3830290.0 GSM8578753 r1 0:150 1:150 A:279487473;C:304130198;G:293947979;T:271501018;N:20332 150 150     279487473 304130198 293947979 271501018 20332 SRX26416437 SRS22936289 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
34031 34031 SRR31031022 SRX26416436 SRS22936290 SRP539182 PRJNA1174121 Quantification of subcellular RNA localization through direct detection of RNA oxidation GSE279714 Other Across cell types and organisms thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled facilitating their biotinylation and purification. However these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq RNAs near a genetically encoded localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package PIGPEN without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm ER and the inner and outer membranes of mitochondria. Finally using transgenic zebrafish we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.   pubmed:39605352;pubmed:40037712   ZF NES GAPDH Rep4 plus GSM8578752   source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing ZF NES GAPDH Rep4 plus OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN. 2 dpf embryos   RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits. HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium. tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF GSM8578752 GSM8578752: ZF NES GAPDH Rep4 plus; Danio rerio; OTHER GSM8578752 r1 GSM8578752 1 RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539182     ZF_NES_GAPDH_Rep4_plus.R1.fq.gz ZF_NES_GAPDH_Rep4_plus.R2.fq.gz fastq fastq 1010253300.0 3367511.0 GSM8578752 r1 0:150 1:150 A:264284161;C:228880831;G:244038984;T:273032130;N:17194 150 150     264284161 228880831 244038984 273032130 17194 SRX26416436 SRS22936290 SRA1993027 Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus                       B B biological fallback assumption illumina novaseq_era full_length random_priming lexogen bulk unknown unknown   United States 2024-10-17 Hatching Embryo Embryo Imprecise All anatomical structures
35567 35567 SRR32928199 SRX28203119 SRS24552825 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 48hpf 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.48.enzymatic.P01.F01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 6 100 100 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.48.enzymatic.P01.F01.fq.gz fastq 800436.0 9529.0 expt2.broad.48.enzymatic.P01.F01.fq.gz 0:84 A:247920;C:168170;G:180799;T:203153;N:394 84       247920 168170 180799 203153 394 SRX28203119 SRS24552825 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 Hatching Embryo Whole Organism All anatomical structures
35568 35568 SRR32928200 SRX28203118 SRS24552823 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 48hpf 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.48.enzymatic.P01.E01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 5 99 99 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.48.enzymatic.P01.E01.fq.gz fastq 496356.0 5909.0 expt2.broad.48.enzymatic.P01.E01.fq.gz 0:84 A:156600;C:99183;G:113282;T:127036;N:255 84       156600 99183 113282 127036 255 SRX28203118 SRS24552823 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 Hatching Embryo Whole Organism All anatomical structures
35569 35569 SRR32928201 SRX28203117 SRS24552824 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 48hpf 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.48.enzymatic.P01.D01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 4 98 98 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.48.enzymatic.P01.D01.fq.gz fastq 2053800.0 24450.0 expt2.broad.48.enzymatic.P01.D01.fq.gz 0:84 A:668634;C:393806;G:431279;T:559022;N:1059 84       668634 393806 431279 559022 1059 SRX28203117 SRS24552824 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 Hatching Embryo Whole Organism All anatomical structures
35570 35570 SRR32928202 SRX28203116 SRS24552821 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 48hpf 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.48.enzymatic.P01.C01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 3 97 97 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.48.enzymatic.P01.C01.fq.gz fastq 2159052.0 25703.0 expt2.broad.48.enzymatic.P01.C01.fq.gz 0:84 A:837784;C:348085;G:463530;T:508544;N:1109 84       837784 348085 463530 508544 1109 SRX28203116 SRS24552821 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 Hatching Embryo Whole Organism All anatomical structures
35571 35571 SRR32928203 SRX28203115 SRS24552822 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 48hpf 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.48.enzymatic.P01.B01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 2 96 96 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.48.enzymatic.P01.B01.fq.gz fastq 3287508.0 39137.0 expt2.broad.48.enzymatic.P01.B01.fq.gz 0:84 A:1090202;C:644484;G:702124;T:848812;N:1886 84       1090202 644484 702124 848812 1886 SRX28203115 SRS24552822 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 Hatching Embryo Whole Organism All anatomical structures
35572 35572 SRR32928204 SRX28203114 SRS24552819 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 48hpf 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.48.enzymatic.P01.A01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 1 95 95 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.48.enzymatic.P01.A01.fq.gz fastq 6623400.0 78850.0 expt2.broad.48.enzymatic.P01.A01.fq.gz 0:84 A:2915935;C:1012732;G:1256523;T:1434621;N:3589 84       2915935 1012732 1256523 1434621 3589 SRX28203114 SRS24552819 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 Hatching Embryo Whole Organism All anatomical structures
35573 35573 SRR32928205 SRX28203113 SRS24552820 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 48hpf 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.48.bead.P18.H02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:16|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 16 94 94 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.48.bead.P18.H02.fq.gz fastq 18079152.0 215228.0 expt2.broad.48.bead.P18.H02.fq.gz 0:84 A:6013555;C:3409380;G:3853431;T:4793252;N:9534 84       6013555 3409380 3853431 4793252 9534 SRX28203113 SRS24552820 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 Hatching Embryo Whole Organism All anatomical structures
35574 35574 SRR32928206 SRX28203112 SRS24552818 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 48hpf 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.48.bead.P18.H01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 15 93 93 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.48.bead.P18.H01.fq.gz fastq 13210764.0 157271.0 expt2.broad.48.bead.P18.H01.fq.gz 0:84 A:4207727;C:2577088;G:2821128;T:3597752;N:7069 84       4207727 2577088 2821128 3597752 7069 SRX28203112 SRS24552818 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 Hatching Embryo Whole Organism All anatomical structures
35575 35575 SRR32928207 SRX28203111 SRS24552817 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 48hpf 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.48.bead.P18.G02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 14 92 92 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.48.bead.P18.G02.fq.gz fastq 14834736.0 176604.0 expt2.broad.48.bead.P18.G02.fq.gz 0:84 A:5041294;C:2753273;G:3108141;T:3924037;N:7991 84       5041294 2753273 3108141 3924037 7991 SRX28203111 SRS24552817 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 Hatching Embryo Whole Organism All anatomical structures
35603 35603 SRR32928234 SRX28203083 SRS24552789 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 48hpf 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.48.bead.P18.G01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 13 91 91 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.48.bead.P18.G01.fq.gz fastq 14202468.0 169077.0 expt2.broad.48.bead.P18.G01.fq.gz 0:84 A:4692822;C:2685182;G:2975257;T:3841545;N:7662 84       4692822 2685182 2975257 3841545 7662 SRX28203083 SRS24552789 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 Hatching Embryo Whole Organism All anatomical structures
35605 35605 SRR32928236 SRX28203081 SRS24552788 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 48hpf 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.48.bead.P18.F02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 12 90 90 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.48.bead.P18.F02.fq.gz fastq 16051728.0 191092.0 expt2.broad.48.bead.P18.F02.fq.gz 0:84 A:5221193;C:3079215;G:3420876;T:4321889;N:8555 84       5221193 3079215 3420876 4321889 8555 SRX28203081 SRS24552788 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 Hatching Embryo Whole Organism All anatomical structures
35606 35606 SRR32928237 SRX28203080 SRS24552786 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 48hpf 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.48.bead.P18.F01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 11 89 89 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.48.bead.P18.F01.fq.gz fastq 19022388.0 226457.0 expt2.broad.48.bead.P18.F01.fq.gz 0:84 A:6375349;C:3646304;G:4032366;T:4958089;N:10280 84       6375349 3646304 4032366 4958089 10280 SRX28203080 SRS24552786 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 Hatching Embryo Whole Organism All anatomical structures
35607 35607 SRR32928238 SRX28203079 SRS24552785 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 48hpf 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.48.bead.P18.E02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 10 88 88 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.48.bead.P18.E02.fq.gz fastq 17436720.0 207580.0 expt2.broad.48.bead.P18.E02.fq.gz 0:84 A:5912075;C:3260546;G:3682832;T:4572094;N:9173 84       5912075 3260546 3682832 4572094 9173 SRX28203079 SRS24552785 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 Hatching Embryo Whole Organism All anatomical structures
35608 35608 SRR32928239 SRX28203078 SRS24552783 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 48hpf 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.48.bead.P18.E01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 9 87 87 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.48.bead.P18.E01.fq.gz fastq 12759768.0 151902.0 expt2.broad.48.bead.P18.E01.fq.gz 0:84 A:4143321;C:2424389;G:2695567;T:3489773;N:6718 84       4143321 2424389 2695567 3489773 6718 SRX28203078 SRS24552783 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 Hatching Embryo Whole Organism All anatomical structures
35609 35609 SRR32928240 SRX28203077 SRS24552784 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 48hpf 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.48.bead.P18.D02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 8 86 86 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.48.bead.P18.D02.fq.gz fastq 17226132.0 205073.0 expt2.broad.48.bead.P18.D02.fq.gz 0:84 A:5722683;C:3229414;G:3698323;T:4566519;N:9193 84       5722683 3229414 3698323 4566519 9193 SRX28203077 SRS24552784 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 Hatching Embryo Whole Organism All anatomical structures
35610 35610 SRR32928241 SRX28203076 SRS24552782 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 48hpf 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.48.bead.P18.D01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 7 85 85 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.48.bead.P18.D01.fq.gz fastq 14390124.0 171311.0 expt2.broad.48.bead.P18.D01.fq.gz 0:84 A:4584304;C:2823369;G:3092301;T:3882609;N:7541 84       4584304 2823369 3092301 3882609 7541 SRX28203076 SRS24552782 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 Hatching Embryo Whole Organism All anatomical structures
35611 35611 SRR32928242 SRX28203075 SRS24552781 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 48hpf 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.48.bead.P18.C02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 6 84 84 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.48.bead.P18.C02.fq.gz fastq 18592560.0 221340.0 expt2.broad.48.bead.P18.C02.fq.gz 0:84 A:6370777;C:3468105;G:3988886;T:4754942;N:9850 84       6370777 3468105 3988886 4754942 9850 SRX28203075 SRS24552781 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 Hatching Embryo Whole Organism All anatomical structures
35612 35612 SRR32928243 SRX28203074 SRS24552780 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 48hpf 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.48.bead.P18.C01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 5 83 83 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.48.bead.P18.C01.fq.gz fastq 12557076.0 149489.0 expt2.broad.48.bead.P18.C01.fq.gz 0:84 A:3977371;C:2443832;G:2711905;T:3417301;N:6667 84       3977371 2443832 2711905 3417301 6667 SRX28203074 SRS24552780 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 Hatching Embryo Whole Organism All anatomical structures
35613 35613 SRR32928244 SRX28203073 SRS24552779 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 48hpf 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.48.bead.P18.B02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 4 82 82 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.48.bead.P18.B02.fq.gz fastq 14289828.0 170117.0 expt2.broad.48.bead.P18.B02.fq.gz 0:84 A:4795697;C:2698305;G:3083373;T:3704963;N:7490 84       4795697 2698305 3083373 3704963 7490 SRX28203073 SRS24552779 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 Hatching Embryo Whole Organism All anatomical structures
35614 35614 SRR32928245 SRX28203072 SRS24552778 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 48hpf 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.48.bead.P18.B01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 3 81 81 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.48.bead.P18.B01.fq.gz fastq 6255144.0 74466.0 expt2.broad.48.bead.P18.B01.fq.gz 0:84 A:1953811;C:1213806;G:1335743;T:1748533;N:3251 84       1953811 1213806 1335743 1748533 3251 SRX28203072 SRS24552778 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 Hatching Embryo Whole Organism All anatomical structures
35616 35616 SRR32928247 SRX28203070 SRS24552776 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 48hpf 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.48.bead.P18.A02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 2 80 80 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.48.bead.P18.A02.fq.gz fastq 16441656.0 195734.0 expt2.broad.48.bead.P18.A02.fq.gz 0:84 A:5495147;C:3127531;G:3493145;T:4317176;N:8657 84       5495147 3127531 3493145 4317176 8657 SRX28203070 SRS24552776 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 Hatching Embryo Whole Organism All anatomical structures
35617 35617 SRR32928248 SRX28203069 SRS24552775 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 48hpf 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.48.bead.P18.A01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 1 79 79 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.48.bead.P18.A01.fq.gz fastq 14319564.0 170471.0 expt2.broad.48.bead.P18.A01.fq.gz 0:84 A:4614154;C:2749141;G:3043759;T:3904988;N:7522 84       4614154 2749141 3043759 3904988 7522 SRX28203069 SRS24552775 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 Hatching Embryo Whole Organism All anatomical structures
35644 35644 SRR32928275 SRX28203042 SRS24552748 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 48hpf 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.48.enzymatic.P01.H01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 8 173 173 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.48.enzymatic.P01.H01.fq.gz fastq 10952424.0 130386.0 expt2.deep.48.enzymatic.P01.H01.fq.gz 0:84 A:3876382;C:2009479;G:2298766;T:2765953;N:1844 84       3876382 2009479 2298766 2765953 1844 SRX28203042 SRS24552748 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 Hatching Embryo Whole Organism All anatomical structures
35645 35645 SRR32928276 SRX28203041 SRS24552747 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 48hpf 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.48.enzymatic.P01.G01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 7 172 172 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.48.enzymatic.P01.G01.fq.gz fastq 14085792.0 167688.0 expt2.deep.48.enzymatic.P01.G01.fq.gz 0:84 A:5224461;C:2624861;G:2935295;T:3298694;N:2481 84       5224461 2624861 2935295 3298694 2481 SRX28203041 SRS24552747 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 Hatching Embryo Whole Organism All anatomical structures
35646 35646 SRR32928277 SRX28203040 SRS24552746 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 48hpf 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.48.enzymatic.P01.F01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 6 171 171 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.48.enzymatic.P01.F01.fq.gz fastq 9595404.0 114231.0 expt2.deep.48.enzymatic.P01.F01.fq.gz 0:84 A:3301852;C:1874682;G:2048715;T:2368498;N:1657 84       3301852 1874682 2048715 2368498 1657 SRX28203040 SRS24552746 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 Hatching Embryo Whole Organism All anatomical structures
35648 35648 SRR32928279 SRX28203038 SRS24552744 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 48hpf 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.48.enzymatic.P01.E01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 5 170 170 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.48.enzymatic.P01.E01.fq.gz fastq 6317472.0 75208.0 expt2.deep.48.enzymatic.P01.E01.fq.gz 0:84 A:2175918;C:1173989;G:1412172;T:1554313;N:1080 84       2175918 1173989 1412172 1554313 1080 SRX28203038 SRS24552744 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 Hatching Embryo Whole Organism All anatomical structures
35649 35649 SRR32928280 SRX28203037 SRS24552743 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 48hpf 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.48.enzymatic.P01.D01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 4 169 169 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.48.enzymatic.P01.D01.fq.gz fastq 26805408.0 319112.0 expt2.deep.48.enzymatic.P01.D01.fq.gz 0:84 A:9489671;C:4847582;G:5421907;T:7041421;N:4827 84       9489671 4847582 5421907 7041421 4827 SRX28203037 SRS24552743 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 Hatching Embryo Whole Organism All anatomical structures
35650 35650 SRR32928281 SRX28203036 SRS24552742 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 48hpf 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.48.enzymatic.P01.C01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 3 168 168 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.48.enzymatic.P01.C01.fq.gz fastq 37386300.0 445075.0 expt2.deep.48.enzymatic.P01.C01.fq.gz 0:84 A:15837274;C:5306422;G:7863430;T:8372443;N:6731 84       15837274 5306422 7863430 8372443 6731 SRX28203036 SRS24552742 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 Hatching Embryo Whole Organism All anatomical structures
35728 35728 SRR32928359 SRX28202958 SRS24552663 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 48hpf 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.48.enzymatic.P01.B01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 2 167 167 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.48.enzymatic.P01.B01.fq.gz fastq 43263192.0 515038.0 expt2.deep.48.enzymatic.P01.B01.fq.gz 0:84 A:15711103;C:7988920;G:8879458;T:10676082;N:7629 84       15711103 7988920 8879458 10676082 7629 SRX28202958 SRS24552663 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 Hatching Embryo Whole Organism All anatomical structures
35729 35729 SRR32928361 SRX28202957 SRS24552664 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 48hpf 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.48.enzymatic.P01.A01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 1 166 166 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.48.enzymatic.P01.A01.fq.gz fastq 111654984.0 1329226.0 expt2.deep.48.enzymatic.P01.A01.fq.gz 0:84 A:50939840;C:16257231;G:20762106;T:23675984;N:19823 84       50939840 16257231 20762106 23675984 19823 SRX28202957 SRS24552664 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 Hatching Embryo Whole Organism All anatomical structures
35730 35730 SRR32928362 SRX28202956 SRS24552662 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 48hpf 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.48.bead.P18.H02.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:16|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 16 165 165 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.48.bead.P18.H02.fq.gz fastq 238250880.0 2836320.0 expt2.deep.48.bead.P18.H02.fq.gz 0:84 A:87774764;C:41601134;G:48854415;T:59978555;N:42012 84       87774764 41601134 48854415 59978555 42012 SRX28202956 SRS24552662 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 Hatching Embryo Whole Organism All anatomical structures
35731 35731 SRR32928363 SRX28202955 SRS24552661 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 48hpf 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.48.bead.P18.H01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 15 164 164 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.48.bead.P18.H01.fq.gz fastq 164680572.0 1960483.0 expt2.deep.48.bead.P18.H01.fq.gz 0:84 A:58086166;C:30009860;G:33521214;T:43034590;N:28742 84       58086166 30009860 33521214 43034590 28742 SRX28202955 SRS24552661 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 Hatching Embryo Whole Organism All anatomical structures
35732 35732 SRR32928364 SRX28202954 SRS24552660 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 48hpf 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.48.bead.P18.G02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 14 163 163 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.48.bead.P18.G02.fq.gz fastq 198828420.0 2367005.0 expt2.deep.48.bead.P18.G02.fq.gz 0:84 A:74768071;C:34197749;G:40014604;T:49812638;N:35358 84       74768071 34197749 40014604 49812638 35358 SRX28202954 SRS24552660 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 Hatching Embryo Whole Organism All anatomical structures
35733 35733 SRR32928365 SRX28202953 SRS24552658 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 48hpf 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.48.bead.P18.G01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 13 162 162 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.48.bead.P18.G01.fq.gz fastq 185114916.0 2203749.0 expt2.deep.48.bead.P18.G01.fq.gz 0:84 A:67685300;C:32656500;G:37099326;T:47641224;N:32566 84       67685300 32656500 37099326 47641224 32566 SRX28202953 SRS24552658 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 Hatching Embryo Whole Organism All anatomical structures
35734 35734 SRR32928366 SRX28202952 SRS24552659 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 48hpf 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.48.bead.P18.F02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 12 161 161 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.48.bead.P18.F02.fq.gz fastq 204337224.0 2432586.0 expt2.deep.48.bead.P18.F02.fq.gz 0:84 A:73860885;C:36257985;G:41424562;T:52758013;N:35779 84       73860885 36257985 41424562 52758013 35779 SRX28202952 SRS24552659 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 Hatching Embryo Whole Organism All anatomical structures
35736 35736 SRR32928368 SRX28202950 SRS24552656 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 48hpf 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.48.bead.P18.F01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 11 160 160 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.48.bead.P18.F01.fq.gz fastq 251949012.0 2999393.0 expt2.deep.48.bead.P18.F01.fq.gz 0:84 A:93851928;C:45256084;G:51250087;T:61546817;N:44096 84       93851928 45256084 51250087 61546817 44096 SRX28202950 SRS24552656 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 Hatching Embryo Whole Organism All anatomical structures
35737 35737 SRR32928369 SRX28202949 SRS24552655 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 48hpf 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.48.bead.P18.E02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 10 159 159 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.48.bead.P18.E02.fq.gz fastq 232932168.0 2773002.0 expt2.deep.48.bead.P18.E02.fq.gz 0:84 A:87509680;C:40423993;G:47439421;T:57518203;N:40871 84       87509680 40423993 47439421 57518203 40871 SRX28202949 SRS24552655 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 Hatching Embryo Whole Organism All anatomical structures
35738 35738 SRR32928370 SRX28202948 SRS24552654 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 48hpf 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.48.bead.P18.E01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 9 158 158 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.48.bead.P18.E01.fq.gz fastq 162318072.0 1932358.0 expt2.deep.48.bead.P18.E01.fq.gz 0:84 A:58032105;C:28749428;G:32874202;T:42634000;N:28337 84       58032105 28749428 32874202 42634000 28337 SRX28202948 SRS24552654 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 Hatching Embryo Whole Organism All anatomical structures
35739 35739 SRR32928371 SRX28202947 SRS24552653 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 48hpf 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.48.bead.P18.D02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 8 157 157 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.48.bead.P18.D02.fq.gz fastq 227115504.0 2703756.0 expt2.deep.48.bead.P18.D02.fq.gz 0:84 A:83596590;C:39343820;G:47110602;T:57023984;N:40508 84       83596590 39343820 47110602 57023984 40508 SRX28202947 SRS24552653 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 Hatching Embryo Whole Organism All anatomical structures
35740 35740 SRR32928372 SRX28202946 SRS24552652 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 48hpf 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.48.bead.P18.D01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 7 156 156 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.48.bead.P18.D01.fq.gz fastq 180858636.0 2153079.0 expt2.deep.48.bead.P18.D01.fq.gz 0:84 A:63790400;C:33184555;G:36908678;T:46943253;N:31750 84       63790400 33184555 36908678 46943253 31750 SRX28202946 SRS24552652 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 Hatching Embryo Whole Organism All anatomical structures
35741 35741 SRR32928373 SRX28202945 SRS24552651 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 48hpf 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.48.bead.P18.C02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 6 155 155 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.48.bead.P18.C02.fq.gz fastq 254836176.0 3033764.0 expt2.deep.48.bead.P18.C02.fq.gz 0:84 A:96800715;C:44151366;G:53186596;T:60652370;N:45129 84       96800715 44151366 53186596 60652370 45129 SRX28202945 SRS24552651 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 Hatching Embryo Whole Organism All anatomical structures
35742 35742 SRR32928374 SRX28202944 SRS24552649 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 48hpf 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.48.bead.P18.C01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 5 154 154 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.48.bead.P18.C01.fq.gz fastq 158669364.0 1888921.0 expt2.deep.48.bead.P18.C01.fq.gz 0:84 A:55554232;C:28711615;G:32786705;T:41589084;N:27728 84       55554232 28711615 32786705 41589084 27728 SRX28202944 SRS24552649 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 Hatching Embryo Whole Organism All anatomical structures
35743 35743 SRR32928375 SRX28202943 SRS24552650 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 48hpf 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.48.bead.P18.B02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 4 153 153 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.48.bead.P18.B02.fq.gz fastq 190474200.0 2267550.0 expt2.deep.48.bead.P18.B02.fq.gz 0:84 A:71029855;C:33202220;G:39545818;T:46662820;N:33487 84       71029855 33202220 39545818 46662820 33487 SRX28202943 SRS24552650 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 Hatching Embryo Whole Organism All anatomical structures
35744 35744 SRR32928376 SRX28202942 SRS24552647 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 48hpf 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.48.bead.P18.B01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 3 152 152 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.48.bead.P18.B01.fq.gz fastq 75929112.0 903918.0 expt2.deep.48.bead.P18.B01.fq.gz 0:84 A:26148298;C:13739979;G:15434234;T:20593156;N:13445 84       26148298 13739979 15434234 20593156 13445 SRX28202942 SRS24552647 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 Hatching Embryo Whole Organism All anatomical structures
35745 35745 SRR32928377 SRX28202941 SRS24552648 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 48hpf 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.48.bead.P18.A02.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 2 151 151 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.48.bead.P18.A02.fq.gz fastq 219828672.0 2617008.0 expt2.deep.48.bead.P18.A02.fq.gz 0:84 A:81458419;C:39095194;G:44843467;T:54392911;N:38681 84       81458419 39095194 44843467 54392911 38681 SRX28202941 SRS24552648 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 Hatching Embryo Whole Organism All anatomical structures
35747 35747 SRR32928379 SRX28202939 SRS24552645 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 48hpf 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.48.bead.P18.A01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf bead dissociation replicate 1 150 150 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.48.bead.P18.A01.fq.gz fastq 180104736.0 2144104.0 expt2.deep.48.bead.P18.A01.fq.gz 0:84 A:64321435;C:32186725;G:36429165;T:47135535;N:31876 84       64321435 32186725 36429165 47135535 31876 SRX28202939 SRS24552645 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 Hatching Embryo Whole Organism All anatomical structures
35775 35775 SRR32928407 SRX28202911 SRS24552617 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 48hpf 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.48.enzymatic.P01.H01.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:48 hpf|dev stage:48 hpf|collection date:2024 01 31|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 48hpf enzymatic dissociation replicate 8 102 102 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.48.enzymatic.P01.H01.fq.gz fastq 876960.0 10440.0 expt2.broad.48.enzymatic.P01.H01.fq.gz 0:84 A:281420;C:174297;G:191202;T:229580;N:461 84       281420 174297 191202 229580 461 SRX28202911 SRS24552617 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 Hatching Embryo Whole Organism All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;