{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Hatching\" and experiment.library_selection = \"other\"", "rows": [[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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 60h 2", "SAMD00028142", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028142", "DRX029551", "Dr 60h 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3875337000.0, 38753370.0, "DRR032745", "0:100 1:0", "A:1042558903;C:899892111;G:896867583;T:1035981420;N:36983", 100, 0, null, null, 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, null, 0.09445, null, 0.66156, null, 0.45564, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 60h 1", "SAMD00028141", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028141", "DRX029550", "Dr 60h 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3538468200.0, 35384682.0, "DRR032744", "0:100 1:0", "A:960664313;C:812459988;G:809014008;T:956295205;N:34686", 100, 0, null, null, 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, null, 0.10346, null, 0.66076, null, 0.45203, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 48h 2", "SAMD00028137", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028137", "DRX029546", "Dr 48h 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3702804700.0, 37028047.0, "DRR032740", "0:100 1:0", "A:993931475;C:862403562;G:857808891;T:988623734;N:37038", 100, 0, null, null, 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, null, 0.08526, null, 0.68349, null, 0.45769, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 48h 1", "SAMD00028136", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028136", "DRX029545", "Dr 48h 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3980240400.0, 39802404.0, "DRR032739", "0:100 1:0", "A:1070497788;C:925240883;G:920038728;T:1064422474;N:40527", 100, 0, null, null, 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, null, 0.08681, null, 0.67874, null, 0.46565, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [7946, "ERR015563", "ERX005934", "ERS012707", "ERP000263", "PRJEB2208", "Zebrafish gene three prime end pull down for genome annotation", "E-MTAB-308", "Transcriptome Analysis", null, null, null, null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "United Kingdom", "2010-08-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, null, null, "zebrafish", "E2 R1", null, "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", null, null, null, null, null, null, null, null, "zebrafish", "9", "9", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "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, null, null, 2186915781, 1920264424, 1996130250, 2141502974, 85853, "SRX26311176", "SRS22839346", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [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", null, null, null, "zebrafish", "E1 R1", null, "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", null, null, null, null, null, null, null, null, "zebrafish", "7", "7", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "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, null, null, 1848193884, 1679679234, 1751186922, 1804529897, 71629, "SRX26311175", "SRS22839344", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [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", null, null, null, "zebrafish", "A3 R1", null, "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", null, null, null, null, null, null, null, null, "zebrafish", "5", "5", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "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, null, null, 2128209130, 1819597773, 1900902610, 2077378388, 82997, "SRX26311174", "SRS22839345", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [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", null, null, null, "zebrafish", "A2 R1", null, "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", null, null, null, null, null, null, null, null, "zebrafish", "3", "3", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "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, null, null, 2121620438, 1812268472, 1879664190, 2076216345, 82329, "SRX26311173", "SRS22839343", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [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", null, null, null, "zebrafish", "E3 R1", null, "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", null, null, null, null, null, null, null, null, "zebrafish", "11", "11", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "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, null, null, 2082463940, 1810596613, 1891675714, 2039730477, 80248, "SRX26311172", "SRS22839342", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [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", null, null, null, "zebrafish", "A1 R1", null, "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", null, null, null, null, null, null, null, null, "zebrafish", "1", "1", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "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, null, null, 2139416119, 1853218216, 1930287523, 2094246996, 81620, "SRX26311171", "SRS22839341", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep4 minus", "GSM8578751", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep3 plus", "GSM8578750", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep3 minus", "GSM8578749", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep2 plus", "GSM8578748", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep2 minus", "GSM8578747", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep1 plus", "GSM8578746", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep1 minus", "GSM8578745", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep4 plus", "GSM8578744", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep4 minus", "GSM8578743", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep3 plus", "GSM8578742", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep3 minus", "GSM8578741", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep2 plus", "GSM8578740", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep2 minus", "GSM8578739", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep1 plus", "GSM8578738", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep1 minus", "GSM8578737", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep4 plus", "GSM8578736", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep4 minus", "GSM8578735", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep3 plus", "GSM8578734", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep3 minus", "GSM8578733", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep2 plus", "GSM8578732", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep2 minus", "GSM8578731", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep1 plus", "GSM8578730", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep1 minus", "GSM8578729", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT pDBF Rep3", "GSM8578770", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT pDBF Rep2", "GSM8578769", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT pDBF Rep1", "GSM8578768", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT mDBF Rep3", "GSM8578767", null, "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", null, "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. 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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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT mDBF Rep2", "GSM8578766", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT mDBF Rep1", "GSM8578765", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb NES pDBF Rep2", "GSM8578764", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb NES pDBF Rep1", "GSM8578763", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb NES mDBF Rep2", "GSM8578762", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb NES mDBF Rep1", "GSM8578761", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep4 plus", "GSM8578760", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep4 minus", "GSM8578759", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep3 plus", "GSM8578758", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep3 minus", "GSM8578757", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep2 plus", "GSM8578756", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep2 minus", "GSM8578755", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep1 plus", "GSM8578754", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep1 minus", "GSM8578753", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep4 plus", "GSM8578752", null, "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", null, "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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.F01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 247920, 168170, 180799, 203153, 394, "SRX28203119", "SRS24552825", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.E01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 156600, 99183, 113282, 127036, 255, "SRX28203118", "SRS24552823", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.D01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 668634, 393806, 431279, 559022, 1059, "SRX28203117", "SRS24552824", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.C01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 837784, 348085, 463530, 508544, 1109, "SRX28203116", "SRS24552821", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.B01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 1090202, 644484, 702124, 848812, 1886, "SRX28203115", "SRS24552822", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "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.", null, "expt2.broad.48.enzymatic.P01.A01.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 2915935, 1012732, 1256523, 1434621, 3589, "SRX28203114", "SRS24552819", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "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.", null, "expt2.broad.48.bead.P18.H02.fq.gz", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "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, null, null, null, 6013555, 3409380, 3853431, 4793252, 9534, "SRX28203113", "SRS24552820", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. 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