run_metadata
482 rows where experiment.library_layout = "PAIRED", technology = "bulk" and tissue_curation = "Whole Organism"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 9699 | 9699 | ERR3301006 | ERX3327073 | ERS3389661 | ERP115040 | PRJEB32363 | RNA seq of zebrafish sa12692 mutants against WT controls | E-MTAB-7920 | Transcriptome Analysis | Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… | WT embryo rep 3 | SAMEA5585437 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway | ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585437|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 3|scientific name:Danio rerio|strain:AB | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:WT embryo rep 3 p | WT embryo rep 3 p | RNA seq of zebrafish sa12692 mutants against WT controls | Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … | Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | NextSeq 500 | ERP115040 | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_2.fq.gz | fastq fastq | 7308473280.0 | 45677958.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo3 | 0:80 1:80 | A:1898812783;C:1731426486;G:1757309247;T:1920031807;N:892957 | 80 | 80 | 1898812783 | 1731426486 | 1757309247 | 1920031807 | 892957 | ERX3327073 | ERS3389661 | ERA1880314 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | 2 | 0.94288 | 0.95671 | 0.07985 | 0.08023 | 0.67915 | 0.67815 | 0.47781 | 0.48461 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||
| 9700 | 9700 | ERR3301005 | ERX3327072 | ERS3389660 | ERP115040 | PRJEB32363 | RNA seq of zebrafish sa12692 mutants against WT controls | E-MTAB-7920 | Transcriptome Analysis | Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… | WT embryo rep 2 | SAMEA5585436 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway | ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585436|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 2|scientific name:Danio rerio|strain:AB | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:WT embryo rep 2 p | WT embryo rep 2 p | RNA seq of zebrafish sa12692 mutants against WT controls | Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … | Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | NextSeq 500 | ERP115040 | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_2.fq.gz | fastq fastq | 7424396000.0 | 46402475.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo2 | 0:80 1:80 | A:1940921070;C:1754354124;G:1768688429;T:1959515088;N:917289 | 80 | 80 | 1940921070 | 1754354124 | 1768688429 | 1959515088 | 917289 | ERX3327072 | ERS3389660 | ERA1880314 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | 2 | 0.94222 | 0.95663 | 0.0909 | 0.09022 | 0.67929 | 0.67606 | 0.48763 | 0.48719 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||
| 9701 | 9701 | ERR3301004 | ERX3327071 | ERS3389659 | ERP115040 | PRJEB32363 | RNA seq of zebrafish sa12692 mutants against WT controls | E-MTAB-7920 | Transcriptome Analysis | Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… | WT embryo rep 1 | SAMEA5585435 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway | ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585435|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 1|scientific name:Danio rerio|strain:AB | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:WT embryo rep 1 p | WT embryo rep 1 p | RNA seq of zebrafish sa12692 mutants against WT controls | Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … | Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | NextSeq 500 | ERP115040 | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_2.fq.gz | fastq fastq | 7300913760.0 | 45630711.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo1 | 0:80 1:80 | A:1931507380;C:1703881934;G:1712942848;T:1951676424;N:905174 | 80 | 80 | 1931507380 | 1703881934 | 1712942848 | 1951676424 | 905174 | ERX3327071 | ERS3389659 | ERA1880314 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | 2 | 0.93831 | 0.95401 | 0.09471 | 0.09526 | 0.67576 | 0.67403 | 0.48092 | 0.48297 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||
| 9705 | 9705 | ERR3301000 | ERX3327067 | ERS3389655 | ERP115040 | PRJEB32363 | RNA seq of zebrafish sa12692 mutants against WT controls | E-MTAB-7920 | Transcriptome Analysis | Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… | Mutant embryo rep 3 | SAMEA5585431 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway | ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585431|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 3|scientific name:Danio rerio|strain:sa12692 mutant | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:Mutant embryo rep 3 p | Mutant embryo rep 3 p | RNA seq of zebrafish sa12692 mutants against WT controls | Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … | Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | NextSeq 500 | ERP115040 | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_2.fq.gz | fastq fastq | 6323854560.0 | 39524091.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo3 | 0:80 1:80 | A:1662088892;C:1473777430;G:1500364334;T:1686853051;N:770853 | 80 | 80 | 1662088892 | 1473777430 | 1500364334 | 1686853051 | 770853 | ERX3327067 | ERS3389655 | ERA1880314 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | 2 | 0.93548 | 0.95404 | 0.09034 | 0.09103 | 0.67584 | 0.67592 | 0.47892 | 0.48193 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||
| 9706 | 9706 | ERR3300999 | ERX3327066 | ERS3389654 | ERP115040 | PRJEB32363 | RNA seq of zebrafish sa12692 mutants against WT controls | E-MTAB-7920 | Transcriptome Analysis | Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… | Mutant embryo rep 2 | SAMEA5585430 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway | ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585430|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 2|scientific name:Danio rerio|strain:sa12692 mutant | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:Mutant embryo rep 2 p | Mutant embryo rep 2 p | RNA seq of zebrafish sa12692 mutants against WT controls | Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … | Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | NextSeq 500 | ERP115040 | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_2.fq.gz | fastq fastq | 6564227680.0 | 41026423.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo2 | 0:80 1:80 | A:1702331829;C:1557343680;G:1583770440;T:1719974488;N:807243 | 80 | 80 | 1702331829 | 1557343680 | 1583770440 | 1719974488 | 807243 | ERX3327066 | ERS3389654 | ERA1880314 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | 2 | 0.94141 | 0.95836 | 0.07518 | 0.07501 | 0.67982 | 0.67803 | 0.47895 | 0.47763 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||
| 9707 | 9707 | ERR3300998 | ERX3327065 | ERS3389653 | ERP115040 | PRJEB32363 | RNA seq of zebrafish sa12692 mutants against WT controls | E-MTAB-7920 | Transcriptome Analysis | Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… | Mutant embryo rep 1 | SAMEA5585429 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway | ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585429|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 1|scientific name:Danio rerio|strain:sa12692 mutant | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:Mutant embryo rep 1 p | Mutant embryo rep 1 p | RNA seq of zebrafish sa12692 mutants against WT controls | Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … | Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | NextSeq 500 | ERP115040 | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 | HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_2.fq.gz | fastq fastq | 6991429280.0 | 43696433.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo1 | 0:80 1:80 | A:1852543850;C:1630880197;G:1635963943;T:1871173669;N:867621 | 80 | 80 | 1852543850 | 1630880197 | 1635963943 | 1871173669 | 867621 | ERX3327065 | ERS3389653 | ERA1880314 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive | 2 | 0.93819 | 0.95201 | 0.10106 | 0.10107 | 0.67541 | 0.67523 | 0.4792 | 0.48253 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||||
| 11226 | 11226 | ERR10368639 | ERX9900562 | ERS13563108 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X9 | SAMEA111469072 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469072|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X9|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X9 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X9 p | 16261X9 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:snrnp70 / | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | 16261X9_190815_A00421_0101_BHFL23DRXX_S2_L001_R1_001.fastq.gz 16261X9_190815_A00421_0101_BHFL23DRXX_S2_L001_R2_001.fastq.gz | fastq fastq | 2686590240.0 | 26339120.0 | E MTAB 12301:16261X9 190815 A00421 0101 BHFL23DRXX S2 L001 R | 0:51 1:51 | A:694597606;C:635153638;G:628248232;T:728333026;N:257738 | 51 | 51 | 694597606 | 635153638 | 628248232 | 728333026 | 257738 | ERX9900562 | ERS13563108 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.94614 | 0.94723 | 0.1538 | 0.15109 | 0.70398 | 0.70352 | 0.48123 | 0.48168 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11227 | 11227 | ERR10368638 | ERX9900561 | ERS13563107 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X8 | SAMEA111469071 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469071|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X8|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X8 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X8 p | 16261X8 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:snrnp70 / | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | 16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R1_001.fastq.gz 16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R2_001.fastq.gz | fastq fastq | 15003930006.0 | 147097353.0 | E MTAB 12301:16261X8 190815 A00421 0101 BHFL23DRXX S4 L001 R | 0:51 1:51 | A:3882939949;C:3570150556;G:3520942177;T:4028462946;N:1434378 | 51 | 51 | 3882939949 | 3570150556 | 3520942177 | 4028462946 | 1434378 | ERX9900561 | ERS13563107 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.94373 | 0.94762 | 0.17954 | 0.17832 | 0.70299 | 0.70207 | 0.48822 | 0.48842 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11228 | 11228 | ERR10368637 | ERX9900560 | ERS13563106 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X7 | SAMEA111469070 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469070|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X7|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X7 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X7 p | 16261X7 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:snrnp70 / | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py | 16261X7_190815_A00421_0101_BHFL23DRXX_S6_L001_R1_001.fastq.gz 16261X7_190815_A00421_0101_BHFL23DRXX_S6_L001_R2_001.fastq.gz | fastq fastq | 3806643060.0 | 37320030.0 | E MTAB 12301:16261X7 190815 A00421 0101 BHFL23DRXX S6 L001 R | 0:51 1:51 | A:971582421;C:919313664;G:905728446;T:1009653865;N:364664 | 51 | 51 | 971582421 | 919313664 | 905728446 | 1009653865 | 364664 | ERX9900560 | ERS13563106 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.94035 | 0.94356 | 0.1661 | 0.16393 | 0.70136 | 0.70082 | 0.48294 | 0.48049 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11229 | 11229 | ERR10368636 | ERX9900559 | ERS13563105 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X6 | SAMEA111469069 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469069|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X6|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X6 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X6 p | 16261X6 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:+/cyt hSNRNP70 | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | 16261X6_190815_A00421_0101_BHFL23DRXX_S7_L001_R1_001.fastq.gz 16261X6_190815_A00421_0101_BHFL23DRXX_S7_L001_R2_001.fastq.gz | fastq fastq | 2875874598.0 | 28194849.0 | E MTAB 12301:16261X6 190815 A00421 0101 BHFL23DRXX S7 L001 R | 0:51 1:51 | A:745870043;C:683782229;G:673037324;T:772909720;N:275282 | 51 | 51 | 745870043 | 683782229 | 673037324 | 772909720 | 275282 | ERX9900559 | ERS13563105 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.9435 | 0.94737 | 0.16987 | 0.16888 | 0.6983 | 0.69826 | 0.47122 | 0.47409 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11230 | 11230 | ERR10368635 | ERX9900558 | ERS13563104 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X5 | SAMEA111469068 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469068|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X5|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X5 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X5 p | 16261X5 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:+/cyt hSNRNP70 | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | 16261X5_190815_A00421_0101_BHFL23DRXX_S8_L001_R1_001.fastq.gz 16261X5_190815_A00421_0101_BHFL23DRXX_S8_L001_R2_001.fastq.gz | fastq fastq | 2656716072.0 | 26046236.0 | E MTAB 12301:16261X5 190815 A00421 0101 BHFL23DRXX S8 L001 R | 0:51 1:51 | A:693979046;C:627484571;G:617505105;T:717493108;N:254242 | 51 | 51 | 693979046 | 627484571 | 617505105 | 717493108 | 254242 | ERX9900558 | ERS13563104 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.94387 | 0.94796 | 0.16299 | 0.16183 | 0.69556 | 0.69581 | 0.46842 | 0.47334 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11231 | 11231 | ERR10368634 | ERX9900557 | ERS13563103 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X4 | SAMEA111469067 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469067|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X4|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X4 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X4 p | 16261X4 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:+/cyt hSNRNP70 | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | 16261X4_190815_A00421_0101_BHFL23DRXX_S9_L001_R1_001.fastq.gz 16261X4_190815_A00421_0101_BHFL23DRXX_S9_L001_R2_001.fastq.gz | fastq fastq | 2693177298.0 | 26403699.0 | E MTAB 12301:16261X4 190815 A00421 0101 BHFL23DRXX S9 L001 R | 0:51 1:51 | A:698547378;C:640687214;G:628869192;T:724816757;N:256757 | 51 | 51 | 698547378 | 640687214 | 628869192 | 724816757 | 256757 | ERX9900557 | ERS13563103 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.94101 | 0.94526 | 0.17344 | 0.17201 | 0.68619 | 0.68513 | 0.47366 | 0.4702 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11232 | 11232 | ERR10368633 | ERX9900556 | ERS13563102 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X3 | SAMEA111469066 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469066|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X3|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X3 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X3 p | 16261X3 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py|options: dnus | 16261X3_190815_A00421_0101_BHFL23DRXX_S10_L001_R1_001.fastq.gz 16261X3_190815_A00421_0101_BHFL23DRXX_S10_L001_R2_001.fastq.gz | fastq fastq | 3104796462.0 | 60878362.0 | E MTAB 12301:16261X3 190815 A00421 0101 BHFL23DRXX S10 L001 R | 0:51 | A:803595677;C:737898133;G:731641815;T:831364716;N:296121 | 51 | 803595677 | 737898133 | 731641815 | 831364716 | 296121 | ERX9900556 | ERS13563102 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 1 | 0.94361 | 0.16161 | 0.69822 | 0.4647 | 51 | B | usable mapping rate | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||
| 11233 | 11233 | ERR10368632 | ERX9900555 | ERS13563101 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X2 | SAMEA111469065 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469065|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X2|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X2 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X2 p | 16261X2 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | 16261X2_190815_A00421_0101_BHFL23DRXX_S11_L001_R1_001.fastq.gz 16261X2_190815_A00421_0101_BHFL23DRXX_S11_L001_R2_001.fastq.gz | fastq fastq | 2935625892.0 | 28780646.0 | E MTAB 12301:16261X2 190815 A00421 0101 BHFL23DRXX S11 L001 R | 0:51 1:51 | A:759844700;C:699591057;G:694530268;T:781380766;N:279101 | 51 | 51 | 759844700 | 699591057 | 694530268 | 781380766 | 279101 | ERX9900555 | ERS13563101 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.93297 | 0.93744 | 0.16748 | 0.16566 | 0.69929 | 0.6996 | 0.4788 | 0.47875 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11234 | 11234 | ERR10368631 | ERX9900554 | ERS13563100 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X12 | SAMEA111469064 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469064|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X12|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X12 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X12 p | 16261X12 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:cyt hSNRNP70/ | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | 16261X12_190815_A00421_0101_BHFL23DRXX_S3_L001_R1_001.fastq.gz 16261X12_190815_A00421_0101_BHFL23DRXX_S3_L001_R2_001.fastq.gz | fastq fastq | 7451469240.0 | 73053620.0 | E MTAB 12301:16261X12 190815 A00421 0101 BHFL23DRXX S3 L001 R | 0:51 1:51 | A:1950856364;C:1747213644;G:1718730947;T:2033957057;N:711228 | 51 | 51 | 1950856364 | 1747213644 | 1718730947 | 2033957057 | 711228 | ERX9900554 | ERS13563100 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.9372 | 0.94118 | 0.20267 | 0.19972 | 0.69794 | 0.69735 | 0.47505 | 0.4883 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11235 | 11235 | ERR10368630 | ERX9900553 | ERS13563099 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X11 | SAMEA111469063 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469063|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X11|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X11 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X11 p | 16261X11 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:cyt hSNRNP70/ | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | 16261X11_190815_A00421_0101_BHFL23DRXX_S5_L001_R1_001.fastq.gz 16261X11_190815_A00421_0101_BHFL23DRXX_S5_L001_R2_001.fastq.gz | fastq fastq | 2754589458.0 | 27005779.0 | E MTAB 12301:16261X11 190815 A00421 0101 BHFL23DRXX S5 L001 R | 0:51 1:51 | A:715675810;C:652231961;G:640938288;T:745480460;N:262939 | 51 | 51 | 715675810 | 652231961 | 640938288 | 745480460 | 262939 | ERX9900553 | ERS13563099 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.93802 | 0.94247 | 0.17937 | 0.17728 | 0.70195 | 0.70067 | 0.48458 | 0.48364 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11236 | 11236 | ERR10368629 | ERX9900552 | ERS13563098 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X10 | SAMEA111469062 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469062|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X10|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X10 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X10 p | 16261X10 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:cyt hSNRNP70/ | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py | 16261X10_190815_A00421_0101_BHFL23DRXX_S1_L001_R1_001.fastq.gz 16261X10_190815_A00421_0101_BHFL23DRXX_S1_L001_R2_001.fastq.gz | fastq fastq | 2319764682.0 | 22742791.0 | E MTAB 12301:16261X10 190815 A00421 0101 BHFL23DRXX S1 L001 R | 0:51 1:51 | A:596937200;C:555502273;G:546190804;T:620912915;N:221490 | 51 | 51 | 596937200 | 555502273 | 546190804 | 620912915 | 221490 | ERX9900552 | ERS13563098 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.94034 | 0.94451 | 0.1621 | 0.16043 | 0.69406 | 0.6928 | 0.4936 | 0.49757 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 11237 | 11237 | ERR10368628 | ERX9900551 | ERS13563097 | ERP141667 | PRJEB56699 | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E-MTAB-12301 | Other | It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 | Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | 16261X1 | SAMEA111469061 | Department of Life Sciences University of Bath | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469061|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X1|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X1 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | E MTAB 12301:16261X1 p | 16261X1 p | RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP141667 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 | ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py | 16261X1_190815_A00421_0101_BHFL23DRXX_S12_L001_R1_001.fastq.gz 16261X1_190815_A00421_0101_BHFL23DRXX_S12_L001_R2_001.fastq.gz | fastq fastq | 2992675512.0 | 29339956.0 | E MTAB 12301:16261X1 190815 A00421 0101 BHFL23DRXX S12 L001 R | 0:51 1:51 | A:768607745;C:718646844;G:713246748;T:791888447;N:285728 | 51 | 51 | 768607745 | 718646844 | 713246748 | 791888447 | 285728 | ERX9900551 | ERS13563097 | ERA18523376 | Department of Life Sciences University of Bath|European Nucleotide Archive | Department of Life Sciences University of Bath|European Nucleotide Archive | 2 | 0.94414 | 0.94881 | 0.16725 | 0.16648 | 0.68909 | 0.68923 | 0.47873 | 0.48244 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2022-10-31 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||
| 15394 | 15394 | ERR12724517 | ERX12099016 | ERS18400121 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 WT 2 | E MTAB 13886:Foxg1 WT 2 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 WT 2 p | Foxg1 WT 2 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X14_200629_A00421_0211_BHN23CDRXX_S26_L001_R1_001.fastq.gz 18067X14_200629_A00421_0211_BHN23CDRXX_S26_L001_R2_001.fastq.gz | fastq fastq | 4054926360.0 | 39754180.0 | E MTAB 13886:18067X14 200629 A00421 0211 BHN23CDRXX S26 L001 R | 0:51 1:51 | A:1027112898;C:978274968;G:992295226;T:1057002684;N:240584 | 51 | 51 | 1027112898 | 978274968 | 992295226 | 1057002684 | 240584 | ERX12099016 | ERS18400121 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15395 | 15395 | ERR12724511 | ERX12099010 | ERS18400115 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 het 9 | E MTAB 13886:Foxg1 het 9 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 het 9 p | Foxg1 het 9 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X11_200629_A00421_0211_BHN23CDRXX_S18_L001_R1_001.fastq.gz 18067X11_200629_A00421_0211_BHN23CDRXX_S18_L001_R2_001.fastq.gz | fastq fastq | 2866917570.0 | 28107035.0 | E MTAB 13886:18067X11 200629 A00421 0211 BHN23CDRXX S18 L001 R | 0:51 1:51 | A:725353172;C:688761995;G:699694713;T:752936948;N:170742 | 51 | 51 | 725353172 | 688761995 | 699694713 | 752936948 | 170742 | ERX12099010 | ERS18400115 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15396 | 15396 | ERR12724513 | ERX12099012 | ERS18400117 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 null 2 | E MTAB 13886:Foxg1 null 2 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a hom|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 null 2 p | Foxg1 null 2 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X2_200629_A00421_0211_BHN23CDRXX_S27_L001_R1_001.fastq.gz 18067X2_200629_A00421_0211_BHN23CDRXX_S27_L001_R2_001.fastq.gz | fastq fastq | 2908778880.0 | 28517440.0 | E MTAB 13886:18067X2 200629 A00421 0211 BHN23CDRXX S27 L001 R | 0:51 1:51 | A:734785178;C:700849624;G:712519278;T:760452796;N:172004 | 51 | 51 | 734785178 | 700849624 | 712519278 | 760452796 | 172004 | ERX12099012 | ERS18400117 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15397 | 15397 | ERR12724507 | ERX12099006 | ERS18400111 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 het 5 | E MTAB 13886:Foxg1 het 5 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 het 5 p | Foxg1 het 5 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X7_200629_A00421_0211_BHN23CDRXX_S19_L001_R1_001.fastq.gz 18067X7_200629_A00421_0211_BHN23CDRXX_S19_L001_R2_001.fastq.gz | fastq fastq | 3111366282.0 | 30503591.0 | E MTAB 13886:18067X7 200629 A00421 0211 BHN23CDRXX S19 L001 R | 0:51 1:51 | A:780094412;C:754603273;G:768441715;T:808041650;N:185232 | 51 | 51 | 780094412 | 754603273 | 768441715 | 808041650 | 185232 | ERX12099006 | ERS18400111 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15398 | 15398 | ERR12724519 | ERX12099018 | ERS18400123 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 WT 6 | E MTAB 13886:Foxg1 WT 6 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 WT 6 p | Foxg1 WT 6 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X16_200629_A00421_0211_BHN23CDRXX_S22_L001_R1_001.fastq.gz 18067X16_200629_A00421_0211_BHN23CDRXX_S22_L001_R2_001.fastq.gz | fastq fastq | 3030554130.0 | 29711315.0 | E MTAB 13886:18067X16 200629 A00421 0211 BHN23CDRXX S22 L001 R | 0:51 1:51 | A:770513445;C:725582256;G:737052763;T:797224111;N:181555 | 51 | 51 | 770513445 | 725582256 | 737052763 | 797224111 | 181555 | ERX12099018 | ERS18400123 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15399 | 15399 | ERR12724510 | ERX12099009 | ERS18400114 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 het 8 | E MTAB 13886:Foxg1 het 8 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 het 8 p | Foxg1 het 8 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X10_200629_A00421_0211_BHN23CDRXX_S13_L001_R1_001.fastq.gz 18067X10_200629_A00421_0211_BHN23CDRXX_S13_L001_R2_001.fastq.gz | fastq fastq | 3601017894.0 | 35304097.0 | E MTAB 13886:18067X10 200629 A00421 0211 BHN23CDRXX S13 L001 R | 0:51 1:51 | A:903986531;C:871550198;G:885398218;T:939870481;N:212466 | 51 | 51 | 903986531 | 871550198 | 885398218 | 939870481 | 212466 | ERX12099009 | ERS18400114 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15400 | 15400 | ERR12724516 | ERX12099015 | ERS18400120 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 WT 1 | E MTAB 13886:Foxg1 WT 1 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 WT 1 p | Foxg1 WT 1 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X13_200629_A00421_0211_BHN23CDRXX_S14_L001_R1_001.fastq.gz 18067X13_200629_A00421_0211_BHN23CDRXX_S14_L001_R2_001.fastq.gz | fastq fastq | 4252867662.0 | 41694781.0 | E MTAB 13886:18067X13 200629 A00421 0211 BHN23CDRXX S14 L001 R | 0:51 1:51 | A:1069523245;C:1031533375;G:1047047746;T:1104513602;N:249694 | 51 | 51 | 1069523245 | 1031533375 | 1047047746 | 1104513602 | 249694 | ERX12099015 | ERS18400120 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15401 | 15401 | ERR12724505 | ERX12099004 | ERS18400109 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 het 2 | E MTAB 13886:Foxg1 het 2 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 het 2 p | Foxg1 het 2 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X5_200629_A00421_0211_BHN23CDRXX_S21_L001_R1_001.fastq.gz 18067X5_200629_A00421_0211_BHN23CDRXX_S21_L001_R2_001.fastq.gz | fastq fastq | 3490870236.0 | 34224218.0 | E MTAB 13886:18067X5 200629 A00421 0211 BHN23CDRXX S21 L001 R | 0:51 1:51 | A:868722737;C:853509703;G:868564192;T:899868487;N:205117 | 51 | 51 | 868722737 | 853509703 | 868564192 | 899868487 | 205117 | ERX12099004 | ERS18400109 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15402 | 15402 | ERR12724509 | ERX12099008 | ERS18400113 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 het 7 | E MTAB 13886:Foxg1 het 7 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 het 7 p | Foxg1 het 7 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X9_200629_A00421_0211_BHN23CDRXX_S15_L001_R1_001.fastq.gz 18067X9_200629_A00421_0211_BHN23CDRXX_S15_L001_R2_001.fastq.gz | fastq fastq | 3288698484.0 | 32242142.0 | E MTAB 13886:18067X9 200629 A00421 0211 BHN23CDRXX S15 L001 R | 0:51 1:51 | A:849623075;C:775307492;G:786016403;T:877557952;N:193562 | 51 | 51 | 849623075 | 775307492 | 786016403 | 877557952 | 193562 | ERX12099008 | ERS18400113 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15403 | 15403 | ERR12724512 | ERX12099011 | ERS18400116 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 null 1 | E MTAB 13886:Foxg1 null 1 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a hom|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 null 1 p | Foxg1 null 1 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X1_200629_A00421_0211_BHN23CDRXX_S28_L001_R1_001.fastq.gz 18067X1_200629_A00421_0211_BHN23CDRXX_S28_L001_R2_001.fastq.gz | fastq fastq | 3735665544.0 | 36624172.0 | E MTAB 13886:18067X1 200629 A00421 0211 BHN23CDRXX S28 L001 R | 0:51 1:51 | A:930463361;C:914183345;G:929494372;T:961303244;N:221222 | 51 | 51 | 930463361 | 914183345 | 929494372 | 961303244 | 221222 | ERX12099011 | ERS18400116 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15404 | 15404 | ERR12724514 | ERX12099013 | ERS18400118 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 null 3 | E MTAB 13886:Foxg1 null 3 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a hom|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 null 3 p | Foxg1 null 3 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X3_200629_A00421_0211_BHN23CDRXX_S25_L001_R1_001.fastq.gz 18067X3_200629_A00421_0211_BHN23CDRXX_S25_L001_R2_001.fastq.gz | fastq fastq | 3581623512.0 | 35113956.0 | E MTAB 13886:18067X3 200629 A00421 0211 BHN23CDRXX S25 L001 R | 0:51 1:51 | A:901782474;C:866330420;G:882309046;T:930988392;N:213180 | 51 | 51 | 901782474 | 866330420 | 882309046 | 930988392 | 213180 | ERX12099013 | ERS18400118 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15405 | 15405 | ERR12724504 | ERX12099003 | ERS18400108 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 het 13 | E MTAB 13886:Foxg1 het 13 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 het 13 p | Foxg1 het 13 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X12_200629_A00421_0211_BHN23CDRXX_S16_L001_R1_001.fastq.gz 18067X12_200629_A00421_0211_BHN23CDRXX_S16_L001_R2_001.fastq.gz | fastq fastq | 3198417570.0 | 31357035.0 | E MTAB 13886:18067X12 200629 A00421 0211 BHN23CDRXX S16 L001 R | 0:51 1:51 | A:806440222;C:774073728;G:785492238;T:832222984;N:188398 | 51 | 51 | 806440222 | 774073728 | 785492238 | 832222984 | 188398 | ERX12099003 | ERS18400108 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15406 | 15406 | ERR12724508 | ERX12099007 | ERS18400112 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 het 6 | E MTAB 13886:Foxg1 het 6 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 het 6 p | Foxg1 het 6 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X8_200629_A00421_0211_BHN23CDRXX_S17_L001_R1_001.fastq.gz 18067X8_200629_A00421_0211_BHN23CDRXX_S17_L001_R2_001.fastq.gz | fastq fastq | 2829840366.0 | 27743533.0 | E MTAB 13886:18067X8 200629 A00421 0211 BHN23CDRXX S17 L001 R | 0:51 1:51 | A:712954704;C:683604864;G:696251651;T:736863084;N:166063 | 51 | 51 | 712954704 | 683604864 | 696251651 | 736863084 | 166063 | ERX12099007 | ERS18400112 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15407 | 15407 | ERR12724506 | ERX12099005 | ERS18400110 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 het 3 | E MTAB 13886:Foxg1 het 3 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 het 3 p | Foxg1 het 3 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X6_200629_A00421_0211_BHN23CDRXX_S20_L001_R1_001.fastq.gz 18067X6_200629_A00421_0211_BHN23CDRXX_S20_L001_R2_001.fastq.gz | fastq fastq | 2947992168.0 | 28901884.0 | E MTAB 13886:18067X6 200629 A00421 0211 BHN23CDRXX S20 L001 R | 0:51 1:51 | A:745555818;C:709342231;G:720902928;T:772016275;N:174916 | 51 | 51 | 745555818 | 709342231 | 720902928 | 772016275 | 174916 | ERX12099005 | ERS18400110 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15408 | 15408 | ERR12724515 | ERX12099014 | ERS18400119 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 null 6 | E MTAB 13886:Foxg1 null 6 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a hom|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 null 6 p | Foxg1 null 6 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X4_200629_A00421_0211_BHN23CDRXX_S23_L001_R1_001.fastq.gz 18067X4_200629_A00421_0211_BHN23CDRXX_S23_L001_R2_001.fastq.gz | fastq fastq | 3166535838.0 | 31044469.0 | E MTAB 13886:18067X4 200629 A00421 0211 BHN23CDRXX S23 L001 R | 0:51 1:51 | A:781063082;C:780685132;G:798403519;T:806197923;N:186182 | 51 | 51 | 781063082 | 780685132 | 798403519 | 806197923 | 186182 | ERX12099014 | ERS18400119 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 15409 | 15409 | ERR12724518 | ERX12099017 | ERS18400122 | ERP158370 | PRJEB73599 | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E-MTAB-13886 | Transcriptome Analysis | Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | Foxg1 WT 5 | E MTAB 13886:Foxg1 WT 5 | isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | E MTAB 13886:Foxg1 WT 5 p | Foxg1 WT 5 p | RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP158370 | Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings | ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 | 18067X15_200629_A00421_0211_BHN23CDRXX_S24_L001_R1_001.fastq.gz 18067X15_200629_A00421_0211_BHN23CDRXX_S24_L001_R2_001.fastq.gz | fastq fastq | 3253306932.0 | 31895166.0 | E MTAB 13886:18067X15 200629 A00421 0211 BHN23CDRXX S24 L001 R | 0:51 1:51 | A:822636212;C:784647591;G:797221431;T:848609081;N:192617 | 51 | 51 | 822636212 | 784647591 | 797221431 | 848609081 | 192617 | ERX12099017 | ERS18400122 | ERA29264914 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | trueseq | bulk | bulk | bulk | United Kingdom | 2024-03-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||||
| 24652 | 24652 | SRR25487068 | SRX21218619 | SRS18475798 | SRP452670 | PRJNA1000968 | CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo | GSE239788 | Transcriptome Analysis | Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq. | pubmed:38114601 | nexn / biological replicate 2 | GSM7673294 | source name:whole organism|tissue:whole organism|genotype:nexn knockout|geo loc name:missing|collection date:missing | nexn / biological replicate 2 | Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value | whole organism | RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics | tissue:whole organism|genotype:nexn knockout | GSM7673294 | GSM7673294: nexn / biological replicate 2; Danio rerio; RNA Seq | GSM7673294 r1 | GSM7673294 | 1 | RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP452670 | loader:fastq load.py | NG-33220_nexn_E2_mut3_lib700540_10254_1_2.fastq.gz NG-33220_nexn_E2_mut3_lib700540_10254_1_1.fastq.gz | fastq fastq | 12821226686.0 | 42454393.0 | GSM7673294 r1 | 0:151 1:151 | A:3460123169;C:2958819646;G:3023309404;T:3378893399;N:81068 | 151 | 151 | 3460123169 | 2958819646 | 3023309404 | 3378893399 | 81068 | SRX21218619 | SRS18475798 | SRA1684694 | Molecular Cardiology, Internal Medicine II, Uniklinik Ulm | Molecular Cardiology, Internal Medicine II, Uniklinik Ulm | 2 | 0.96544 | 0.96684 | 0.07136 | 0.06827 | 0.66969 | 0.66914 | 0.44957 | 0.45604 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | full_length | random_priming | unknown | bulk | bulk | bulk | Germany | 2023-08-01 | Undetermined | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 24653 | 24653 | SRR25487069 | SRX21218618 | SRS18475797 | SRP452670 | PRJNA1000968 | CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo | GSE239788 | Transcriptome Analysis | Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq. | pubmed:38114601 | nexn / biological replicate 1 | GSM7673293 | source name:whole organism|tissue:whole organism|genotype:nexn knockout|geo loc name:missing|collection date:missing | nexn / biological replicate 1 | Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value | whole organism | RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics | tissue:whole organism|genotype:nexn knockout | GSM7673293 | GSM7673293: nexn / biological replicate 1; Danio rerio; RNA Seq | GSM7673293 r1 | GSM7673293 | 1 | RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP452670 | loader:fastq load.py | NG-33220_nexn_E2_mut1_lib691942_10222_3_2.fastq.gz NG-33220_nexn_E2_mut1_lib691942_10222_3_1.fastq.gz | fastq fastq | 6518650974.0 | 21584937.0 | GSM7673293 r1 | 0:151 1:151 | A:1776227735;C:1486881610;G:1503672330;T:1751641678;N:227621 | 151 | 151 | 1776227735 | 1486881610 | 1503672330 | 1751641678 | 227621 | SRX21218618 | SRS18475797 | SRA1684694 | Molecular Cardiology, Internal Medicine II, Uniklinik Ulm | Molecular Cardiology, Internal Medicine II, Uniklinik Ulm | 2 | 0.9619 | 0.96365 | 0.08223 | 0.07902 | 0.66967 | 0.66811 | 0.44763 | 0.45022 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | full_length | random_priming | unknown | bulk | bulk | bulk | Germany | 2023-08-01 | Undetermined | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 24654 | 24654 | SRR25487070 | SRX21218617 | SRS18475796 | SRP452670 | PRJNA1000968 | CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo | GSE239788 | Transcriptome Analysis | Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq. | pubmed:38114601 | nexn+/+ biological replicate 2 | GSM7673292 | source name:whole organism|tissue:whole organism|genotype:WT|geo loc name:missing|collection date:missing | nexn+/+ biological replicate 2 | Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value | whole organism | RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics | tissue:whole organism|genotype:WT | GSM7673292 | GSM7673292: nexn+/+ biological replicate 2; Danio rerio; RNA Seq | GSM7673292 r1 | GSM7673292 | 1 | RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP452670 | loader:fastq load.py | NG-33220_nexn_E2_sib3_lib693760_10227_1_1.fastq.gz NG-33220_nexn_E2_sib3_lib693760_10227_1_2.fastq.gz | fastq fastq | 9966559304.0 | 33001852.0 | GSM7673292 r1 | 0:151 1:151 | A:2799666848;C:2201108797;G:2237142072;T:2728542087;N:99500 | 151 | 151 | 2799666848 | 2201108797 | 2237142072 | 2728542087 | 99500 | SRX21218617 | SRS18475796 | SRA1684694 | Molecular Cardiology, Internal Medicine II, Uniklinik Ulm | Molecular Cardiology, Internal Medicine II, Uniklinik Ulm | 2 | 0.95433 | 0.9562 | 0.11378 | 0.10948 | 0.68426 | 0.68302 | 0.45622 | 0.46107 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | full_length | random_priming | unknown | bulk | bulk | bulk | Germany | 2023-08-01 | Undetermined | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 24655 | 24655 | SRR25487071 | SRX21218616 | SRS18475795 | SRP452670 | PRJNA1000968 | CRISPR/Cas9 mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo | GSE239788 | Transcriptome Analysis | Nexilin NEXN plays a crucial role in stabilizing the sarcomeric Z disk of striated muscle fibers and when mutated leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. We characterized a constitutive homozygous CRISPR/Cas9 mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably in contrast to nexn morphants CRISPR/Cas9 nexn / knockout embryos showed a milder phenotype without xxx development of a pronounced pericardial edema or blood congestion. nexn specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn / knockout embryos. Overall design: To investigate the influence of nexn knockout on cardiac and skeletal muslce we generated a CRISPR/Cas9 mediated nexn knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA seq. | pubmed:38114601 | nexn+/+ biological replicate 1 | GSM7673291 | source name:whole organism|tissue:whole organism|genotype:WT|geo loc name:missing|collection date:missing | nexn+/+ biological replicate 1 | Raw sequencing data is screened for reads originating from rRNA using RiboDetector eurofins genomics INVIEW transcriptome High quality sequence reads are aligned to the reference genome using STAR Spliced Transcripts Alignment to a Reference run through Sentieon framework along with the known gene models. eurofins genomics INVIEW transcriptome Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. eurofins genomics INVIEW transcriptome Assembly: GRCz11 Supplementary files format and content: Sample wise gene wise read counts TPM value and FPKM value | whole organism | RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics | tissue:whole organism|genotype:WT | GSM7673291 | GSM7673291: nexn+/+ biological replicate 1; Danio rerio; RNA Seq | GSM7673291 r1 | GSM7673291 | 1 | RNA was extracted using the Qiagen RNeasy Mini Kit. 1 25 µg total RNA was used for library preparation. INVIEW transcriptome done by eurofins Genomics | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP452670 | loader:fastq load.py | NG-33220_nexn_E2_sib2_lib693759_10227_2_1.fastq.gz NG-33220_nexn_E2_sib2_lib693759_10227_2_2.fastq.gz | fastq fastq | 13610380470.0 | 45067485.0 | GSM7673291 r1 | 0:151 1:151 | A:3776423931;C:3037607848;G:3100752195;T:3694688167;N:908329 | 151 | 151 | 3776423931 | 3037607848 | 3100752195 | 3694688167 | 908329 | SRX21218616 | SRS18475795 | SRA1684694 | Molecular Cardiology, Internal Medicine II, Uniklinik Ulm | Molecular Cardiology, Internal Medicine II, Uniklinik Ulm | 2 | 0.95714 | 0.95793 | 0.10127 | 0.09788 | 0.69445 | 0.69278 | 0.47084 | 0.46602 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | full_length | random_priming | unknown | bulk | bulk | bulk | Germany | 2023-08-01 | Undetermined | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 30749 | 30749 | SRR30167500 | SRX25634206 | SRS22278604 | SRP495323 | PRJNA1088158 | Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. | GSE261646 | Transcriptome Analysis | The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee… | pubmed:39302832 | pCas13d al1 4hpf rep3 | GSM8446429 | source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing | pCas13d al1 4hpf rep3 | Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates | Whole embryo | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF | GSM8446429 | GSM8446429: pCas13d al1 4hpf rep3; Danio rerio; RNA Seq | GSM8446429 r1 | GSM8446429 | 1 | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP495323 | L67855_S11_L001_R1_001.fastq.gz L67855_S11_L001_R2_001.fastq.gz | fastq fastq | 2565767500.0 | 25657675.0 | GSM8446429 r1 | 0:50 1:50 | A:676771006;C:596998503;G:603560859;T:688437132;N:0 | 50 | 50 | 676771006 | 596998503 | 603560859 | 688437132 | 0 | SRX25634206 | SRS22278604 | SRA1942483 | Computational Biology, Stowers Institute for Medical Research | Computational Biology, Stowers Institute for Medical Research | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2024-08-07 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 30750 | 30750 | SRR30167501 | SRX25634205 | SRS22278605 | SRP495323 | PRJNA1088158 | Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. | GSE261646 | Transcriptome Analysis | The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee… | pubmed:39302832 | pCas13d al1 4hpf rep2 | GSM8446428 | source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing | pCas13d al1 4hpf rep2 | Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates | Whole embryo | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF | GSM8446428 | GSM8446428: pCas13d al1 4hpf rep2; Danio rerio; RNA Seq | GSM8446428 r1 | GSM8446428 | 1 | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP495323 | L67854_S10_L001_R1_001.fastq.gz L67854_S10_L001_R2_001.fastq.gz | fastq fastq | 2528276500.0 | 25282765.0 | GSM8446428 r1 | 0:50 1:50 | A:664250318;C:589008342;G:598067975;T:676949865;N:0 | 50 | 50 | 664250318 | 589008342 | 598067975 | 676949865 | 0 | SRX25634205 | SRS22278605 | SRA1942483 | Computational Biology, Stowers Institute for Medical Research | Computational Biology, Stowers Institute for Medical Research | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2024-08-07 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 30751 | 30751 | SRR30167502 | SRX25634204 | SRS22278602 | SRP495323 | PRJNA1088158 | Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. | GSE261646 | Transcriptome Analysis | The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee… | pubmed:39302832 | pCas13d al1 4hpf rep1 | GSM8446427 | source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing | pCas13d al1 4hpf rep1 | Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates | Whole embryo | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF | GSM8446427 | GSM8446427: pCas13d al1 4hpf rep1; Danio rerio; RNA Seq | GSM8446427 r1 | GSM8446427 | 1 | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP495323 | L67853_S9_L001_R1_001.fastq.gz L67853_S9_L001_R2_001.fastq.gz | fastq fastq | 2416897800.0 | 24168978.0 | GSM8446427 r1 | 0:50 1:50 | A:636467903;C:563622671;G:568978039;T:647829187;N:0 | 50 | 50 | 636467903 | 563622671 | 568978039 | 647829187 | 0 | SRX25634204 | SRS22278602 | SRA1942483 | Computational Biology, Stowers Institute for Medical Research | Computational Biology, Stowers Institute for Medical Research | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2024-08-07 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 30752 | 30752 | SRR30167503 | SRX25634203 | SRS22278601 | SRP495323 | PRJNA1088158 | Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. | GSE261646 | Transcriptome Analysis | The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee… | pubmed:39302832 | znf281b KD 4hpf rep3 | GSM8446426 | source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing | znf281b KD 4hpf rep3 | Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates | Whole embryo | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF | GSM8446426 | GSM8446426: znf281b KD 4hpf rep3; Danio rerio; RNA Seq | GSM8446426 r1 | GSM8446426 | 1 | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP495323 | L67851_S7_L001_R1_001.fastq.gz L67851_S7_L001_R2_001.fastq.gz | fastq fastq | 2366597500.0 | 23665975.0 | GSM8446426 r1 | 0:50 1:50 | A:620883932;C:547989723;G:563335901;T:634387944;N:0 | 50 | 50 | 620883932 | 547989723 | 563335901 | 634387944 | 0 | SRX25634203 | SRS22278601 | SRA1942483 | Computational Biology, Stowers Institute for Medical Research | Computational Biology, Stowers Institute for Medical Research | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2024-08-07 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 30753 | 30753 | SRR30167504 | SRX25634202 | SRS22278600 | SRP495323 | PRJNA1088158 | Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. | GSE261646 | Transcriptome Analysis | The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee… | pubmed:39302832 | znf281b KD 4hpf rep2 | GSM8446425 | source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing | znf281b KD 4hpf rep2 | Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates | Whole embryo | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF | GSM8446425 | GSM8446425: znf281b KD 4hpf rep2; Danio rerio; RNA Seq | GSM8446425 r1 | GSM8446425 | 1 | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP495323 | L67850_S6_L001_R1_001.fastq.gz L67850_S6_L001_R2_001.fastq.gz | fastq fastq | 2497293900.0 | 24972939.0 | GSM8446425 r1 | 0:50 1:50 | A:657452880;C:579618079;G:589789328;T:670433613;N:0 | 50 | 50 | 657452880 | 579618079 | 589789328 | 670433613 | 0 | SRX25634202 | SRS22278600 | SRA1942483 | Computational Biology, Stowers Institute for Medical Research | Computational Biology, Stowers Institute for Medical Research | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2024-08-07 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 30754 | 30754 | SRR30167505 | SRX25634201 | SRS22278596 | SRP495323 | PRJNA1088158 | Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. | GSE261646 | Transcriptome Analysis | The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee… | pubmed:39302832 | znf281b KD 4hpf rep1 | GSM8446424 | source name:Whole embryo|tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing | znf281b KD 4hpf rep1 | Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates | Whole embryo | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | tissue:Whole embryo|developmental stage:4hpf|genotype:AB TF and TLF | GSM8446424 | GSM8446424: znf281b KD 4hpf rep1; Danio rerio; RNA Seq | GSM8446424 r1 | GSM8446424 | 1 | Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish znf281b knockdown embryos… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP495323 | L67849_S5_L001_R1_001.fastq.gz L67849_S5_L001_R2_001.fastq.gz | fastq fastq | 2607154500.0 | 26071545.0 | GSM8446424 r1 | 0:50 1:50 | A:685092511;C:605305852;G:618493032;T:698263105;N:0 | 50 | 50 | 685092511 | 605305852 | 618493032 | 698263105 | 0 | SRX25634201 | SRS22278596 | SRA1942483 | Computational Biology, Stowers Institute for Medical Research | Computational Biology, Stowers Institute for Medical Research | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2024-08-07 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32033 | 32033 | SRR28976522 | SRX24505963 | SRS21254128 | SRP506702 | PRJNA1109723 | rbm24a is an organizer component of germ plasm to determine germ cell fate | GSE267086 | Other | The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish. | Zebrafish RIP seq Rbm24a Knock in IP | GSM8259538 | source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP|geo loc name:missing|collection date:missing | Zebrafish RIP seq Rbm24a Knock in IP | Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP | GSM8259538 | GSM8259538: Zebrafish RIP seq Rbm24a Knock in IP; Danio rerio; RIP Seq | GSM8259538 r1 | GSM8259538 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RIP-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP506702 | RIP_KI_IP_R2.fq.gz RIP_KI_IP_R1.fq.gz | fastq fastq | 6457893104.0 | 21383752.0 | GSM8259538 r1 | 0:151 1:151 | A:975588225;C:2019180290;G:2469634919;T:992947702;N:541968 | 151 | 151 | 975588225 | 2019180290 | 2469634919 | 992947702 | 541968 | SRX24505963 | SRS21254128 | SRA1863578 | Ang Li, College of Life Sciences, shandong university | Ang Li, College of Life Sciences, shandong university | 2 | 0.90304 | 0.86018 | 0.20083 | 0.20471 | 0.96382 | 0.96743 | 0.96102 | 0.98876 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-05-09 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||
| 32034 | 32034 | SRR28976523 | SRX24505962 | SRS21254127 | SRP506702 | PRJNA1109723 | rbm24a is an organizer component of germ plasm to determine germ cell fate | GSE267086 | Other | The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish. | Zebrafish RIP seq wild type IP | GSM8259537 | source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP|geo loc name:missing|collection date:missing | Zebrafish RIP seq wild type IP | Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP | GSM8259537 | GSM8259537: Zebrafish RIP seq wild type IP; Danio rerio; RIP Seq | GSM8259537 r1 | GSM8259537 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RIP-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP506702 | RIP_WT_IP_R2.fq.gz RIP_WT_IP_R1.fq.gz | fastq fastq | 4501412680.0 | 14905340.0 | GSM8259537 r1 | 0:151 1:151 | A:651609366;C:1285679784;G:1901211768;T:662533141;N:378621 | 151 | 151 | 651609366 | 1285679784 | 1901211768 | 662533141 | 378621 | SRX24505962 | SRS21254127 | SRA1863578 | Ang Li, College of Life Sciences, shandong university | Ang Li, College of Life Sciences, shandong university | 2 | 0.96426 | 0.81361 | 0.26579 | 0.2253 | 0.97784 | 0.97806 | 0.8699 | 0.93379 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-05-09 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||
| 32035 | 32035 | SRR28976524 | SRX24505961 | SRS21254126 | SRP506702 | PRJNA1109723 | rbm24a is an organizer component of germ plasm to determine germ cell fate | GSE267086 | Other | The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish. | Zebrafish RIP seq Rbm24a Knock in input | GSM8259536 | source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input|geo loc name:missing|collection date:missing | Zebrafish RIP seq Rbm24a Knock in input | Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input | GSM8259536 | GSM8259536: Zebrafish RIP seq Rbm24a Knock in input; Danio rerio; RIP Seq | GSM8259536 r1 | GSM8259536 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RIP-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP506702 | RIP_KI_Input_R2.fq.gz RIP_KI_Input_R1.fq.gz | fastq fastq | 9539398726.0 | 31587413.0 | GSM8259536 r1 | 0:151 1:151 | A:2233069830;C:2078359171;G:3009942870;T:2217201959;N:824896 | 151 | 151 | 2233069830 | 2078359171 | 3009942870 | 2217201959 | 824896 | SRX24505961 | SRS21254126 | SRA1863578 | Ang Li, College of Life Sciences, shandong university | Ang Li, College of Life Sciences, shandong university | 2 | 0.90112 | 0.81448 | 0.02415 | 0.01993 | 0.79287 | 0.79807 | 0.47884 | 0.48186 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-05-09 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||
| 32036 | 32036 | SRR28976525 | SRX24505960 | SRS21254125 | SRP506702 | PRJNA1109723 | rbm24a is an organizer component of germ plasm to determine germ cell fate | GSE267086 | Other | The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish. | Zebrafish RIP seq wild type input | GSM8259535 | source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input|geo loc name:missing|collection date:missing | Zebrafish RIP seq wild type input | Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input | GSM8259535 | GSM8259535: Zebrafish RIP seq wild type input; Danio rerio; RIP Seq | GSM8259535 r1 | GSM8259535 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RIP-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP506702 | RIP_WT_Input_R2.fq.gz RIP_WT_Input_R1.fq.gz | fastq fastq | 14180410302.0 | 46955001.0 | GSM8259535 r1 | 0:151 1:151 | A:3380011534;C:2883841476;G:4593876270;T:3321465622;N:1215400 | 151 | 151 | 3380011534 | 2883841476 | 4593876270 | 3321465622 | 1215400 | SRX24505960 | SRS21254125 | SRA1863578 | Ang Li, College of Life Sciences, shandong university | Ang Li, College of Life Sciences, shandong university | 2 | 0.86497 | 0.64685 | 0.04432 | 0.02854 | 0.79324 | 0.8031 | 0.52927 | 0.53304 | 151 | 151 | B | B | mate2-mate1 similar by mapping diff | illumina | novaseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-05-09 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||
| 32138 | 32138 | SRR29068704 | SRX24593115 | SRS21331205 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R242H/R242H 0 Gy biol rep 3 | GSM8275261 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 R242H/R242H 0 Gy biol rep 3 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:0 Gy | GSM8275261 | GSM8275261: tp53 R242H/R242H 0 Gy biol rep 3; Danio rerio; RNA Seq | GSM8275261 r1 | GSM8275261 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 242N-3_R1_001.fastq.gz 242N-3_R2_001.fastq.gz | fastq fastq | 3756026400.0 | 12520088.0 | GSM8275261 r1 | 0:150 1:150 | A:1041832393;C:829828422;G:875135132;T:1008888364;N:342089 | 150 | 150 | 1041832393 | 829828422 | 875135132 | 1008888364 | 342089 | SRX24593115 | SRS21331205 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32139 | 32139 | SRR29068705 | SRX24593114 | SRS21331204 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R242H/R242H 0 Gy biol rep 2 | GSM8275260 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 R242H/R242H 0 Gy biol rep 2 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:0 Gy | GSM8275260 | GSM8275260: tp53 R242H/R242H 0 Gy biol rep 2; Danio rerio; RNA Seq | GSM8275260 r1 | GSM8275260 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 242N-2_R1_001.fastq.gz 242N-2_R2_001.fastq.gz | fastq fastq | 11625588300.0 | 38751961.0 | GSM8275260 r1 | 0:150 1:150 | A:3060988139;C:2752201460;G:2833688238;T:2978620952;N:89511 | 150 | 150 | 3060988139 | 2752201460 | 2833688238 | 2978620952 | 89511 | SRX24593114 | SRS21331204 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32140 | 32140 | SRR29068706 | SRX24593113 | SRS21331203 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R242H/R242H 0 Gy biol rep 1 | GSM8275259 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 R242H/R242H 0 Gy biol rep 1 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:0 Gy | GSM8275259 | GSM8275259: tp53 R242H/R242H 0 Gy biol rep 1; Danio rerio; RNA Seq | GSM8275259 r1 | GSM8275259 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 242N-1_R1_001.fastq.gz 242N-1_R2_001.fastq.gz | fastq fastq | 16753656300.0 | 55845521.0 | GSM8275259 r1 | 0:150 1:150 | A:4617320633;C:3760731037;G:3904182758;T:4471291288;N:130584 | 150 | 150 | 4617320633 | 3760731037 | 3904182758 | 4471291288 | 130584 | SRX24593113 | SRS21331203 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32141 | 32141 | SRR29068707 | SRX24593112 | SRS21331202 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R242H/R242H 30 Gy biol rep 3 | GSM8275258 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 R242H/R242H 30 Gy biol rep 3 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:30 Gy | GSM8275258 | GSM8275258: tp53 R242H/R242H 30 Gy biol rep 3; Danio rerio; RNA Seq | GSM8275258 r1 | GSM8275258 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 242I-3_R1_001.fastq.gz 242I-3_R2_001.fastq.gz | fastq fastq | 9248979000.0 | 30829930.0 | GSM8275258 r1 | 0:150 1:150 | A:2490790601;C:2140065573;G:2202142508;T:2415909359;N:70959 | 150 | 150 | 2490790601 | 2140065573 | 2202142508 | 2415909359 | 70959 | SRX24593112 | SRS21331202 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32142 | 32142 | SRR29068708 | SRX24593111 | SRS21331201 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R242H/R242H 30 Gy biol rep 2 | GSM8275257 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 R242H/R242H 30 Gy biol rep 2 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:30 Gy | GSM8275257 | GSM8275257: tp53 R242H/R242H 30 Gy biol rep 2; Danio rerio; RNA Seq | GSM8275257 r1 | GSM8275257 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 242I-2_R1_001.fastq.gz 242I-2_R2_001.fastq.gz | fastq fastq | 14876409900.0 | 49588033.0 | GSM8275257 r1 | 0:150 1:150 | A:4155568434;C:3275443734;G:3414514883;T:4028089617;N:2793232 | 150 | 150 | 4155568434 | 3275443734 | 3414514883 | 4028089617 | 2793232 | SRX24593111 | SRS21331201 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32143 | 32143 | SRR29068709 | SRX24593110 | SRS21331200 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R242H/R242H 30 Gy biol rep 1 | GSM8275256 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 R242H/R242H 30 Gy biol rep 1 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R242H/R242H|treatment:30 Gy | GSM8275256 | GSM8275256: tp53 R242H/R242H 30 Gy biol rep 1; Danio rerio; RNA Seq | GSM8275256 r1 | GSM8275256 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 242I-1_R1_001.fastq.gz 242I-1_R2_001.fastq.gz | fastq fastq | 13181905500.0 | 43939685.0 | GSM8275256 r1 | 0:150 1:150 | A:3680992920;C:2900884646;G:3025183249;T:3572297095;N:2547590 | 150 | 150 | 3680992920 | 2900884646 | 3025183249 | 3572297095 | 2547590 | SRX24593110 | SRS21331200 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32144 | 32144 | SRR29068710 | SRX24593109 | SRS21331199 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R217H/R217H 0 Gy biol rep 3 | GSM8275255 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 R217H/R217H 0 Gy biol rep 3 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:0 Gy | GSM8275255 | GSM8275255: tp53 R217H/R217H 0 Gy biol rep 3; Danio rerio; RNA Seq | GSM8275255 r1 | GSM8275255 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 217N-3_R1_001.fastq.gz 217N-3_R2_001.fastq.gz | fastq fastq | 15270830700.0 | 50902769.0 | GSM8275255 r1 | 0:150 1:150 | A:4143520783;C:3507470789;G:3602468084;T:4017251797;N:119247 | 150 | 150 | 4143520783 | 3507470789 | 3602468084 | 4017251797 | 119247 | SRX24593109 | SRS21331199 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32145 | 32145 | SRR29068711 | SRX24593108 | SRS21331198 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R217H/R217H 0 Gy biol rep 2 | GSM8275254 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 R217H/R217H 0 Gy biol rep 2 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:0 Gy | GSM8275254 | GSM8275254: tp53 R217H/R217H 0 Gy biol rep 2; Danio rerio; RNA Seq | GSM8275254 r1 | GSM8275254 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 217N-2_R1_001.fastq.gz 217N-2_R2_001.fastq.gz | fastq fastq | 11979598500.0 | 39931995.0 | GSM8275254 r1 | 0:150 1:150 | A:3377772889;C:2602459474;G:2731248324;T:3266053178;N:2064635 | 150 | 150 | 3377772889 | 2602459474 | 2731248324 | 3266053178 | 2064635 | SRX24593108 | SRS21331198 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32146 | 32146 | SRR29068712 | SRX24593107 | SRS21331197 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R217H/R217H 0 Gy biol rep 1 | GSM8275253 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 R217H/R217H 0 Gy biol rep 1 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:0 Gy | GSM8275253 | GSM8275253: tp53 R217H/R217H 0 Gy biol rep 1; Danio rerio; RNA Seq | GSM8275253 r1 | GSM8275253 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 217N-1_R1_001.fastq.gz 217N-1_R2_001.fastq.gz | fastq fastq | 15189213300.0 | 50630711.0 | GSM8275253 r1 | 0:150 1:150 | A:3119274866;C:4485924650;G:4554332809;T:3029563736;N:117239 | 150 | 150 | 3119274866 | 4485924650 | 4554332809 | 3029563736 | 117239 | SRX24593107 | SRS21331197 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32147 | 32147 | SRR29068713 | SRX24593106 | SRS21331196 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R217H/R217H 30 Gy biol rep 3 | GSM8275252 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 R217H/R217H 30 Gy biol rep 3 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:30 Gy | GSM8275252 | GSM8275252: tp53 R217H/R217H 30 Gy biol rep 3; Danio rerio; RNA Seq | GSM8275252 r1 | GSM8275252 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 217I-3_R1_001.fastq.gz 217I-3_R2_001.fastq.gz | fastq fastq | 9626255400.0 | 32087518.0 | GSM8275252 r1 | 0:150 1:150 | A:2534842583;C:2272553595;G:2345492999;T:2473292717;N:73506 | 150 | 150 | 2534842583 | 2272553595 | 2345492999 | 2473292717 | 73506 | SRX24593106 | SRS21331196 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32148 | 32148 | SRR29068714 | SRX24593105 | SRS21331195 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R217H/R217H 30 Gy biol rep 2 | GSM8275251 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 R217H/R217H 30 Gy biol rep 2 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:30 Gy | GSM8275251 | GSM8275251: tp53 R217H/R217H 30 Gy biol rep 2; Danio rerio; RNA Seq | GSM8275251 r1 | GSM8275251 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 217I-2_R1_001.fastq.gz 217I-2_R2_001.fastq.gz | fastq fastq | 13102529400.0 | 43675098.0 | GSM8275251 r1 | 0:150 1:150 | A:3679606150;C:2816108752;G:3037629807;T:3569081166;N:103525 | 150 | 150 | 3679606150 | 2816108752 | 3037629807 | 3569081166 | 103525 | SRX24593105 | SRS21331195 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32149 | 32149 | SRR29068715 | SRX24593104 | SRS21331194 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 R217H/R217H 30 Gy biol rep 1 | GSM8275250 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 R217H/R217H 30 Gy biol rep 1 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:tp53 R217H/R217H|treatment:30 Gy | GSM8275250 | GSM8275250: tp53 R217H/R217H 30 Gy biol rep 1; Danio rerio; RNA Seq | GSM8275250 r1 | GSM8275250 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | 217I-1_R1_001.fastq.gz 217I-1_R2_001.fastq.gz | fastq fastq | 14318813100.0 | 47729377.0 | GSM8275250 r1 | 0:150 1:150 | A:4016220509;C:3121053092;G:3260389642;T:3917828243;N:3321614 | 150 | 150 | 4016220509 | 3121053092 | 3260389642 | 3917828243 | 3321614 | SRX24593104 | SRS21331194 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32150 | 32150 | SRR29068716 | SRX24593103 | SRS21331193 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 null/null 0 Gy biol rep 3 | GSM8275249 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 null/null 0 Gy biol rep 3 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:0 Gy | GSM8275249 | GSM8275249: tp53 null/null 0 Gy biol rep 3; Danio rerio; RNA Seq | GSM8275249 r1 | GSM8275249 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | NN-3_R1_001.fastq.gz NN-3_R2_001.fastq.gz | fastq fastq | 9280014900.0 | 30933383.0 | GSM8275249 r1 | 0:150 1:150 | A:2579418683;C:2021325576;G:2174123842;T:2505074465;N:72334 | 150 | 150 | 2579418683 | 2021325576 | 2174123842 | 2505074465 | 72334 | SRX24593103 | SRS21331193 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32151 | 32151 | SRR29068717 | SRX24593102 | SRS21331192 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 null/null 0 Gy biol rep 2 | GSM8275248 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 null/null 0 Gy biol rep 2 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:0 Gy | GSM8275248 | GSM8275248: tp53 null/null 0 Gy biol rep 2; Danio rerio; RNA Seq | GSM8275248 r1 | GSM8275248 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | NN-2_R1_001.fastq.gz NN-2_R2_001.fastq.gz | fastq fastq | 10707389700.0 | 35691299.0 | GSM8275248 r1 | 0:150 1:150 | A:2996008142;C:2309486822;G:2484070965;T:2917739315;N:84456 | 150 | 150 | 2996008142 | 2309486822 | 2484070965 | 2917739315 | 84456 | SRX24593102 | SRS21331192 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32152 | 32152 | SRR29068718 | SRX24593101 | SRS21331191 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 null/null 0 Gy biol rep 1 | GSM8275247 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:0 Gy|geo loc name:missing|collection date:missing | tp53 null/null 0 Gy biol rep 1 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:0 Gy | GSM8275247 | GSM8275247: tp53 null/null 0 Gy biol rep 1; Danio rerio; RNA Seq | GSM8275247 r1 | GSM8275247 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | NN-1_R1_001.fastq.gz NN-1_R2_001.fastq.gz | fastq fastq | 7135635900.0 | 23785453.0 | GSM8275247 r1 | 0:150 1:150 | A:2013858781;C:1536736753;G:1635489625;T:1949495108;N:55633 | 150 | 150 | 2013858781 | 1536736753 | 1635489625 | 1949495108 | 55633 | SRX24593101 | SRS21331191 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32153 | 32153 | SRR29068719 | SRX24593100 | SRS21331190 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 null/null 30 Gy biol rep 3 | GSM8275246 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 null/null 30 Gy biol rep 3 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:30 Gy | GSM8275246 | GSM8275246: tp53 null/null 30 Gy biol rep 3; Danio rerio; RNA Seq | GSM8275246 r1 | GSM8275246 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | NI-3_R1_001.fastq.gz NI-3_R2_001.fastq.gz | fastq fastq | 8705985900.0 | 29019953.0 | GSM8275246 r1 | 0:150 1:150 | A:2451599576;C:1903967773;G:1979058961;T:2371292759;N:66831 | 150 | 150 | 2451599576 | 1903967773 | 1979058961 | 2371292759 | 66831 | SRX24593100 | SRS21331190 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32154 | 32154 | SRR29068720 | SRX24593099 | SRS21331189 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 null/null 30 Gy biol rep 2 | GSM8275245 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 null/null 30 Gy biol rep 2 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:30 Gy | GSM8275245 | GSM8275245: tp53 null/null 30 Gy biol rep 2; Danio rerio; RNA Seq | GSM8275245 r1 | GSM8275245 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | NI-2_R1_001.fastq.gz NI-2_R2_001.fastq.gz | fastq fastq | 4040556000.0 | 13468520.0 | GSM8275245 r1 | 0:150 1:150 | A:1064729231;C:885920482;G:1092301122;T:997572075;N:33090 | 150 | 150 | 1064729231 | 885920482 | 1092301122 | 997572075 | 33090 | SRX24593099 | SRS21331189 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32155 | 32155 | SRR29068721 | SRX24593098 | SRS21331188 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | tp53 null/null 30 Gy biol rep 1 | GSM8275244 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:30 Gy|geo loc name:missing|collection date:missing | tp53 null/null 30 Gy biol rep 1 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:CG1|genotype:tp53 null/null|treatment:30 Gy | GSM8275244 | GSM8275244: tp53 null/null 30 Gy biol rep 1; Danio rerio; RNA Seq | GSM8275244 r1 | GSM8275244 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | NI-1_R1_001.fastq.gz NI-1_R2_001.fastq.gz | fastq fastq | 13228044600.0 | 44093482.0 | GSM8275244 r1 | 0:150 1:150 | A:3648277896;C:2853778984;G:3204527446;T:3521354654;N:105620 | 150 | 150 | 3648277896 | 2853778984 | 3204527446 | 3521354654 | 105620 | SRX24593098 | SRS21331188 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32156 | 32156 | SRR29068722 | SRX24593097 | SRS21331187 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | casper 0 Gy biol rep 3 | GSM8275243 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:0 Gy|geo loc name:missing|collection date:missing | casper 0 Gy biol rep 3 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:0 Gy | GSM8275243 | GSM8275243: casper 0 Gy biol rep 3; Danio rerio; RNA Seq | GSM8275243 r1 | GSM8275243 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | CN-3_R1_001.fastq.gz CN-3_R2_001.fastq.gz | fastq fastq | 17305790400.0 | 57685968.0 | GSM8275243 r1 | 0:150 1:150 | A:4943405723;C:3677509037;G:3849406622;T:4830939454;N:4529564 | 150 | 150 | 4943405723 | 3677509037 | 3849406622 | 4830939454 | 4529564 | SRX24593097 | SRS21331187 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32157 | 32157 | SRR29068723 | SRX24593096 | SRS21331186 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | casper 0 Gy biol rep 2 | GSM8275242 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:0 Gy|geo loc name:missing|collection date:missing | casper 0 Gy biol rep 2 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:0 Gy | GSM8275242 | GSM8275242: casper 0 Gy biol rep 2; Danio rerio; RNA Seq | GSM8275242 r1 | GSM8275242 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | CN-2_R1_001.fastq.gz CN-2_R2_001.fastq.gz | fastq fastq | 7856126700.0 | 26187089.0 | GSM8275242 r1 | 0:150 1:150 | A:2181800519;C:1712717950;G:1835053315;T:2126491645;N:63271 | 150 | 150 | 2181800519 | 1712717950 | 1835053315 | 2126491645 | 63271 | SRX24593096 | SRS21331186 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32158 | 32158 | SRR29068724 | SRX24593095 | SRS21331185 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | casper 0 Gy biol rep 1 | GSM8275241 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:0 Gy|geo loc name:missing|collection date:missing | casper 0 Gy biol rep 1 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:0 Gy | GSM8275241 | GSM8275241: casper 0 Gy biol rep 1; Danio rerio; RNA Seq | GSM8275241 r1 | GSM8275241 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | CN-1_R1_001.fastq.gz CN-1_R2_001.fastq.gz | fastq fastq | 17854583700.0 | 59515279.0 | GSM8275241 r1 | 0:150 1:150 | A:5047426493;C:3817702039;G:4070868393;T:4913755567;N:4831208 | 150 | 150 | 5047426493 | 3817702039 | 4070868393 | 4913755567 | 4831208 | SRX24593095 | SRS21331185 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32159 | 32159 | SRR29068725 | SRX24593094 | SRS21331184 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | casper 30 Gy biol rep 3 | GSM8275240 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:30 Gy|geo loc name:missing|collection date:missing | casper 30 Gy biol rep 3 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:30 Gy | GSM8275240 | GSM8275240: casper 30 Gy biol rep 3; Danio rerio; RNA Seq | GSM8275240 r1 | GSM8275240 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | CI-3_R1_001.fastq.gz CI-3_R2_001.fastq.gz | fastq fastq | 7459084200.0 | 24863614.0 | GSM8275240 r1 | 0:150 1:150 | A:2017184252;C:1711102783;G:1772264422;T:1958475306;N:57437 | 150 | 150 | 2017184252 | 1711102783 | 1772264422 | 1958475306 | 57437 | SRX24593094 | SRS21331184 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32160 | 32160 | SRR29068726 | SRX24593093 | SRS21331183 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | casper 30 Gy biol rep 2 | GSM8275239 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:30 Gy|geo loc name:missing|collection date:missing | casper 30 Gy biol rep 2 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:30 Gy | GSM8275239 | GSM8275239: casper 30 Gy biol rep 2; Danio rerio; RNA Seq | GSM8275239 r1 | GSM8275239 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | CI-2_R1_001.fastq.gz CI-2_R2_001.fastq.gz | fastq fastq | 9754545900.0 | 32515153.0 | GSM8275239 r1 | 0:150 1:150 | A:2528054076;C:2339919668;G:2442835629;T:2443659385;N:77142 | 150 | 150 | 2528054076 | 2339919668 | 2442835629 | 2443659385 | 77142 | SRX24593093 | SRS21331183 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 32161 | 32161 | SRR29068727 | SRX24593092 | SRS21331182 | SRP508364 | PRJNA1112809 | tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [RNA seq] | GSE267760 | Transcriptome Analysis | Li Fraumeni syndrome LFS is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants human R248 and R273H. These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically we have shown that the R217H and R242H alleles result in partial to no activation of key p53 target genes are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 month of age. Tumor histology resembles human sarcomas a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants suggesting it is a more aggressive mutation while the R217H allele may be hypomorphic. Additionally we observed mutation specific differences both in the tumor type and sex bias across tp53 null R217H and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles impacting metabolism cell signalling and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS. Overall design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers tp53 R217H and R242H human R248 and R273 using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab Ignatius et al. 2018. We also used the transparent casper strain as a comparis… | casper 30 Gy biol rep 1 | GSM8275238 | source name:whole embryo|tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:30 Gy|geo loc name:missing|collection date:missing | casper 30 Gy biol rep 1 | The RNA Seq data were mapped with STAR v2.7 to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation. Assembly: GRCz11 Supplementary files format and content: tab delinated text file includes count matrix with each sample | whole embryo | Larvae were exposed to either 0 or 30 Gy of irradiation at xxx hpf. | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | Larvae were maintained at 28C and samples were collected at 30 hpf. | tissue:whole embryo|Stage:30 hpf|strain:AB|genotype:casper|treatment:30 Gy | GSM8275238 | GSM8275238: casper 30 Gy biol rep 1; Danio rerio; RNA Seq | GSM8275238 r1 | GSM8275238 | 1 | Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine MS 222 and homogenized in 500μL TRIzol reagent Life Technologies 15596026 using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct zol RNA MicroPrep kit Zymo Research Corperation R2060. 4ug of total RNA from each sample were sent for RNA sequencing. RNA Libraries were constructed for standard paired read RNA sequencing by GeneWiz. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP508364 | loader:fastq load.py | CI-1_R1_001.fastq.gz CI-1_R2_001.fastq.gz | fastq fastq | 8075614200.0 | 26918714.0 | GSM8275238 r1 | 0:150 1:150 | A:2167921413;C:1845510317;G:1962119169;T:2100000616;N:62685 | 150 | 150 | 2167921413 | 1845510317 | 1962119169 | 2100000616 | 62685 | SRX24593092 | SRS21331182 | Berman Lab, Children's Hospital of Eastern Ontario Research Institute | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Canada | 2024-05-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34032 | 34032 | SRR31033342 | SRX26418811 | SRS22938447 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish Riboseq M sphere 5 | GSM8579734 | source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish Riboseq M sphere 5 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579734 | GSM8579734: Zebrafish Riboseq M sphere 5; Danio rerio; RNA Seq | GSM8579734 r1 | GSM8579734 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-sphere-5_L1_1.fq.gz M-sphere-5_L1_2.fq.gz | fastq fastq | 6386202900.0 | 21287343.0 | GSM8579734 r1 | 0:150 1:150 | A:1749323046;C:1447024706;G:1497348312;T:1692462495;N:44341 | 150 | 150 | 1749323046 | 1447024706 | 1497348312 | 1692462495 | 44341 | SRX26418811 | SRS22938447 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34033 | 34033 | SRR31033343 | SRX26418810 | SRS22938444 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish Riboseq M sphere 4 | GSM8579733 | source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish Riboseq M sphere 4 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579733 | GSM8579733: Zebrafish Riboseq M sphere 4; Danio rerio; RNA Seq | GSM8579733 r1 | GSM8579733 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-sphere-4_L1_1.fq.gz M-sphere-4_L1_2.fq.gz | fastq fastq | 7329708000.0 | 24432360.0 | GSM8579733 r1 | 0:150 1:150 | A:1999459748;C:1667498786;G:1726069847;T:1936629080;N:50539 | 150 | 150 | 1999459748 | 1667498786 | 1726069847 | 1936629080 | 50539 | SRX26418810 | SRS22938444 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34034 | 34034 | SRR31033344 | SRX26418809 | SRS22938445 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish Riboseq M sphere 2 | GSM8579732 | source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish Riboseq M sphere 2 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579732 | GSM8579732: Zebrafish Riboseq M sphere 2; Danio rerio; RNA Seq | GSM8579732 r1 | GSM8579732 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-sphere-2_L1_1.fq.gz M-sphere-2_L1_2.fq.gz | fastq fastq | 6614502300.0 | 22048341.0 | GSM8579732 r1 | 0:150 1:150 | A:1811784017;C:1496173021;G:1549885996;T:1756614738;N:44528 | 150 | 150 | 1811784017 | 1496173021 | 1549885996 | 1756614738 | 44528 | SRX26418809 | SRS22938445 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34035 | 34035 | SRR31033352 | SRX26418808 | SRS22938439 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish Riboseq M sphere 1 | GSM8579731 | source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish Riboseq M sphere 1 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579731 | GSM8579731: Zebrafish Riboseq M sphere 1; Danio rerio; RNA Seq | GSM8579731 r1 | GSM8579731 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-sphere-1_L1_1.fq.gz M-sphere-1_L1_2.fq.gz | fastq fastq | 7080587100.0 | 23601957.0 | GSM8579731 r1 | 0:150 1:150 | A:1946013215;C:1594400814;G:1652448966;T:1887676214;N:47891 | 150 | 150 | 1946013215 | 1594400814 | 1652448966 | 1887676214 | 47891 | SRX26418808 | SRS22938439 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34036 | 34036 | SRR31033345 | SRX26418807 | SRS22938440 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish Riboseq M 4cell 5 | GSM8579730 | source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish Riboseq M 4cell 5 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579730 | GSM8579730: Zebrafish Riboseq M 4cell 5; Danio rerio; RNA Seq | GSM8579730 r1 | GSM8579730 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-4cell-5_L1_1.fq.gz M-4cell-5_L1_2.fq.gz | fastq fastq | 5643278100.0 | 18810927.0 | GSM8579730 r1 | 0:150 1:150 | A:1555401034;C:1268722567;G:1323837426;T:1495279385;N:37688 | 150 | 150 | 1555401034 | 1268722567 | 1323837426 | 1495279385 | 37688 | SRX26418807 | SRS22938440 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Cleavage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34037 | 34037 | SRR31033351 | SRX26418806 | SRS22938443 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish Riboseq M 4cell 4 | GSM8579729 | source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish Riboseq M 4cell 4 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579729 | GSM8579729: Zebrafish Riboseq M 4cell 4; Danio rerio; RNA Seq | GSM8579729 r1 | GSM8579729 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-4cell-4_L1_1.fq.gz M-4cell-4_L1_2.fq.gz | fastq fastq | 6607232100.0 | 22024107.0 | GSM8579729 r1 | 0:150 1:150 | A:1825603885;C:1480833466;G:1538474482;T:1762276005;N:44262 | 150 | 150 | 1825603885 | 1480833466 | 1538474482 | 1762276005 | 44262 | SRX26418806 | SRS22938443 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Cleavage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34038 | 34038 | SRR31033346 | SRX26418805 | SRS22938438 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish Riboseq M 4cell 3 | GSM8579728 | source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish Riboseq M 4cell 3 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579728 | GSM8579728: Zebrafish Riboseq M 4cell 3; Danio rerio; RNA Seq | GSM8579728 r1 | GSM8579728 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-4cell-3_L1_1.fq.gz M-4cell-3_L1_2.fq.gz | fastq fastq | 7948794900.0 | 26495983.0 | GSM8579728 r1 | 0:150 1:150 | A:2183592013;C:1794605656;G:1863773539;T:2106770087;N:53605 | 150 | 150 | 2183592013 | 1794605656 | 1863773539 | 2106770087 | 53605 | SRX26418805 | SRS22938438 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Cleavage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34039 | 34039 | SRR31033350 | SRX26418804 | SRS22938441 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish Riboseq M 4cell 2 | GSM8579727 | source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish Riboseq M 4cell 2 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579727 | GSM8579727: Zebrafish Riboseq M 4cell 2; Danio rerio; RNA Seq | GSM8579727 r1 | GSM8579727 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-4cell-2_L1_1.fq.gz M-4cell-2_L1_2.fq.gz | fastq fastq | 7036510200.0 | 23455034.0 | GSM8579727 r1 | 0:150 1:150 | A:1830698676;C:1686461802;G:1754202163;T:1765099649;N:47910 | 150 | 150 | 1830698676 | 1686461802 | 1754202163 | 1765099649 | 47910 | SRX26418804 | SRS22938441 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Cleavage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34040 | 34040 | SRR31033347 | SRX26418803 | SRS22938435 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq M 24HPF 4 | GSM8579726 | source name:whole embryo|tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish RNAseq M 24HPF 4 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579726 | GSM8579726: Zebrafish RNAseq M 24HPF 4; Danio rerio; RNA Seq | GSM8579726 r1 | GSM8579726 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-24HPF-4_L1_1.fq.gz M-24HPF-4_L1_2.fq.gz | fastq fastq | 7509691500.0 | 25032305.0 | GSM8579726 r1 | 0:150 1:150 | A:2051155577;C:1703307330;G:1761930893;T:1993247939;N:49761 | 150 | 150 | 2051155577 | 1703307330 | 1761930893 | 1993247939 | 49761 | SRX26418803 | SRS22938435 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34041 | 34041 | SRR31033348 | SRX26418802 | SRS22938442 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq M 24HPF 2 | GSM8579724 | source name:whole embryo|tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish RNAseq M 24HPF 2 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579724 | GSM8579724: Zebrafish RNAseq M 24HPF 2; Danio rerio; RNA Seq | GSM8579724 r1 | GSM8579724 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-24HPF-2_L1_1.fq.gz M-24HPF-2_L1_2.fq.gz | fastq fastq | 7108870200.0 | 23696234.0 | GSM8579724 r1 | 0:150 1:150 | A:1938248034;C:1616546428;G:1672221476;T:1881804827;N:49435 | 150 | 150 | 1938248034 | 1616546428 | 1672221476 | 1881804827 | 49435 | SRX26418802 | SRS22938442 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34042 | 34042 | SRR31033349 | SRX26418801 | SRS22938437 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq M 24HPF 3 | GSM8579725 | source name:whole embryo|tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish RNAseq M 24HPF 3 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579725 | GSM8579725: Zebrafish RNAseq M 24HPF 3; Danio rerio; RNA Seq | GSM8579725 r1 | GSM8579725 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-24HPF-3_L1_1.fq.gz M-24HPF-3_L1_2.fq.gz | fastq fastq | 6652426200.0 | 22174754.0 | GSM8579725 r1 | 0:150 1:150 | A:1801675309;C:1524819778;G:1581222646;T:1744664175;N:44292 | 150 | 150 | 1801675309 | 1524819778 | 1581222646 | 1744664175 | 44292 | SRX26418801 | SRS22938437 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34043 | 34043 | SRR31033353 | SRX26418800 | SRS22938434 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq M 24HPF 1 | GSM8579723 | source name:whole embryo|tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing | Zebrafish RNAseq M 24HPF 1 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a | GSM8579723 | GSM8579723: Zebrafish RNAseq M 24HPF 1; Danio rerio; RNA Seq | GSM8579723 r1 | GSM8579723 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | M-24HPF-1_L1_1.fq.gz M-24HPF-1_L1_2.fq.gz | fastq fastq | 5665772400.0 | 18885908.0 | GSM8579723 r1 | 0:150 1:150 | A:1531867787;C:1299623555;G:1349456236;T:1484786200;N:38622 | 150 | 150 | 1531867787 | 1299623555 | 1349456236 | 1484786200 | 38622 | SRX26418800 | SRS22938434 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34044 | 34044 | SRR31033360 | SRX26418799 | SRS22938436 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq Sibling sphere 4 | GSM8579722 | source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq Sibling sphere 4 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type | GSM8579722 | GSM8579722: Zebrafish RNAseq Sibling sphere 4; Danio rerio; RNA Seq | GSM8579722 r1 | GSM8579722 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-sphere-4_L1_1.fq.gz Sibling-sphere-4_L1_2.fq.gz | fastq fastq | 7056333000.0 | 23521110.0 | GSM8579722 r1 | 0:150 1:150 | A:1940035016;C:1589047995;G:1648953235;T:1878249310;N:47444 | 150 | 150 | 1940035016 | 1589047995 | 1648953235 | 1878249310 | 47444 | SRX26418799 | SRS22938436 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34045 | 34045 | SRR31033354 | SRX26418798 | SRS22938429 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq Sibling sphere 3 | GSM8579721 | source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq Sibling sphere 3 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type | GSM8579721 | GSM8579721: Zebrafish RNAseq Sibling sphere 3; Danio rerio; RNA Seq | GSM8579721 r1 | GSM8579721 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-sphere-3_L1_1.fq.gz Sibling-sphere-3_L1_2.fq.gz | fastq fastq | 7102058100.0 | 23673527.0 | GSM8579721 r1 | 0:150 1:150 | A:1932660580;C:1619713195;G:1685329939;T:1864306893;N:47493 | 150 | 150 | 1932660580 | 1619713195 | 1685329939 | 1864306893 | 47493 | SRX26418798 | SRS22938429 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34046 | 34046 | SRR31033359 | SRX26418797 | SRS22938433 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq Sibling sphere 1 | GSM8579720 | source name:whole embryo|tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq Sibling sphere 1 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:sphere stage|cell type:embryonic cell|genotype:wild type | GSM8579720 | GSM8579720: Zebrafish RNAseq Sibling sphere 1; Danio rerio; RNA Seq | GSM8579720 r1 | GSM8579720 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-sphere-1_L1_1.fq.gz Sibling-sphere-1_L1_2.fq.gz | fastq fastq | 6375563100.0 | 21251877.0 | GSM8579720 r1 | 0:150 1:150 | A:1748656292;C:1440631635;G:1494630558;T:1691601145;N:43470 | 150 | 150 | 1748656292 | 1440631635 | 1494630558 | 1691601145 | 43470 | SRX26418797 | SRS22938433 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Blastula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34047 | 34047 | SRR31033355 | SRX26418796 | SRS22938428 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq Sibling 4cell 4 | GSM8579719 | source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq Sibling 4cell 4 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type | GSM8579719 | GSM8579719: Zebrafish RNAseq Sibling 4cell 4; Danio rerio; RNA Seq | GSM8579719 r1 | GSM8579719 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-4cell-4_L1_1.fq.gz Sibling-4cell-4_L1_2.fq.gz | fastq fastq | 7424662500.0 | 24748875.0 | GSM8579719 r1 | 0:150 1:150 | A:2045351766;C:1671617139;G:1731338149;T:1976305596;N:49850 | 150 | 150 | 2045351766 | 1671617139 | 1731338149 | 1976305596 | 49850 | SRX26418796 | SRS22938428 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Cleavage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34048 | 34048 | SRR31033358 | SRX26418795 | SRS22938431 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq Sibling 4cell 2 | GSM8579718 | source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq Sibling 4cell 2 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type | GSM8579718 | GSM8579718: Zebrafish RNAseq Sibling 4cell 2; Danio rerio; RNA Seq | GSM8579718 r1 | GSM8579718 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-4cell-2_L1_1.fq.gz Sibling-4cell-2_L1_2.fq.gz | fastq fastq | 6484454400.0 | 21614848.0 | GSM8579718 r1 | 0:150 1:150 | A:1701212104;C:1544478776;G:1597991536;T:1640728663;N:43321 | 150 | 150 | 1701212104 | 1544478776 | 1597991536 | 1640728663 | 43321 | SRX26418795 | SRS22938431 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Cleavage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34049 | 34049 | SRR31033356 | SRX26418794 | SRS22938430 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq Sibling 4cell 1 | GSM8579717 | source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq Sibling 4cell 1 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type | GSM8579717 | GSM8579717: Zebrafish RNAseq Sibling 4cell 1; Danio rerio; RNA Seq | GSM8579717 r1 | GSM8579717 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-4cell-1_L1_1.fq.gz Sibling-4cell-1_L1_2.fq.gz | fastq fastq | 8126999700.0 | 27089999.0 | GSM8579717 r1 | 0:150 1:150 | A:2195769442;C:1872416059;G:1934390760;T:2124367874;N:55565 | 150 | 150 | 2195769442 | 1872416059 | 1934390760 | 2124367874 | 55565 | SRX26418794 | SRS22938430 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Cleavage | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34050 | 34050 | SRR31033357 | SRX26418793 | SRS22938426 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq lSibling 24HPF 5 | GSM8579716 | source name:whole embryo|tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq lSibling 24HPF 5 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:wild type | GSM8579716 | GSM8579716: Zebrafish RNAseq lSibling 24HPF 5; Danio rerio; RNA Seq | GSM8579716 r1 | GSM8579716 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-24HPF-5_L1_1.fq.gz Sibling-24HPF-5_L1_2.fq.gz | fastq fastq | 6064473600.0 | 20214912.0 | GSM8579716 r1 | 0:150 1:150 | A:1656555504;C:1376598854;G:1427079525;T:1604199064;N:40653 | 150 | 150 | 1656555504 | 1376598854 | 1427079525 | 1604199064 | 40653 | SRX26418793 | SRS22938426 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34051 | 34051 | SRR31033361 | SRX26418792 | SRS22938432 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq lSibling 24HPF 4 | GSM8579715 | source name:whole embryo|tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq lSibling 24HPF 4 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:wild type | GSM8579715 | GSM8579715: Zebrafish RNAseq lSibling 24HPF 4; Danio rerio; RNA Seq | GSM8579715 r1 | GSM8579715 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-24HPF-4_L1_1.fq.gz Sibling-24HPF-4_L1_2.fq.gz | fastq fastq | 7707809400.0 | 25692698.0 | GSM8579715 r1 | 0:150 1:150 | A:2085012024;C:1773253808;G:1833941298;T:2015550481;N:51789 | 150 | 150 | 2085012024 | 1773253808 | 1833941298 | 2015550481 | 51789 | SRX26418792 | SRS22938432 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34052 | 34052 | SRR31033362 | SRX26418791 | SRS22938427 | SRP539223 | PRJNA1174207 | Rbm24 dictates mRNA recruitment for germ plasm assembly | GSE279756 | Transcriptome Analysis | Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf. | Zebrafish RNAseq lSibling 24HPF 3 | GSM8579714 | source name:whole embryo|tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing | Zebrafish RNAseq lSibling 24HPF 3 | Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample | whole embryo | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. | Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C | tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:wild type | GSM8579714 | GSM8579714: Zebrafish RNAseq lSibling 24HPF 3; Danio rerio; RNA Seq | GSM8579714 r1 | GSM8579714 | 1 | Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP539223 | Sibling-24HPF-3_L1_1.fq.gz Sibling-24HPF-3_L1_2.fq.gz | fastq fastq | 6177886500.0 | 20592955.0 | GSM8579714 r1 | 0:150 1:150 | A:1693766114;C:1396254520;G:1447264824;T:1640559782;N:41260 | 150 | 150 | 1693766114 | 1396254520 | 1447264824 | 1640559782 | 41260 | SRX26418791 | SRS22938427 | SRA1993092 | Shandong university | Shandong university | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | China | 2024-10-17 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||||||||||||||
| 34364 | 34364 | SRR31695142 | SRX27056958 | SRS23518718 | SRP551059 | PRJNA1197382 | Enhanced RNA targeting CRISPR Cas technology in zebrafish V | GSE284120 | Transcriptome Analysis | Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized | parent bioproject:PRJNA1128082 | pubmed:40091120 | RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4 | GSM8678154 | source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing | RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4 | Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample | whole embryo | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA | GSM8678154 | GSM8678154: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4; Danio rerio; RNA Seq | GSM8678154 r1 | GSM8678154 | 1 | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ELEMENT | Element AVITI | SRP551059 | T_pRfxCas13d_g1Syn_rep4_R1.fastq.gz T_pRfxCas13d_g1Syn_rep4_R2.fastq.gz | fastq fastq | 1869396000.0 | 12462640.0 | GSM8678154 r1 | 0:75 1:75 | A:497545631;C:434254877;G:436435676;T:501090064;N:69752 | 75 | 75 | 497545631 | 434254877 | 436435676 | 501090064 | 69752 | SRX27056958 | SRS23518718 | SRA2032641 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | B | B | biological fallback assumption | element | element | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2024-12-12 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||
| 34365 | 34365 | SRR31695143 | SRX27056957 | SRS23518717 | SRP551059 | PRJNA1197382 | Enhanced RNA targeting CRISPR Cas technology in zebrafish V | GSE284120 | Transcriptome Analysis | Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized | parent bioproject:PRJNA1128082 | pubmed:40091120 | RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3 | GSM8678153 | source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing | RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3 | Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample | whole embryo | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA | GSM8678153 | GSM8678153: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3; Danio rerio; RNA Seq | GSM8678153 r1 | GSM8678153 | 1 | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ELEMENT | Element AVITI | SRP551059 | T_pRfxCas13d_g1Syn_rep3_R1.fastq.gz T_pRfxCas13d_g1Syn_rep3_R2.fastq.gz | fastq fastq | 1939758450.0 | 12931723.0 | GSM8678153 r1 | 0:75 1:75 | A:510928336;C:455303431;G:458245636;T:515206838;N:74209 | 75 | 75 | 510928336 | 455303431 | 458245636 | 515206838 | 74209 | SRX27056957 | SRS23518717 | SRA2032641 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | B | B | biological fallback assumption | element | element | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2024-12-12 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||
| 34366 | 34366 | SRR31695144 | SRX27056956 | SRS23518716 | SRP551059 | PRJNA1197382 | Enhanced RNA targeting CRISPR Cas technology in zebrafish V | GSE284120 | Transcriptome Analysis | Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized | parent bioproject:PRJNA1128082 | pubmed:40091120 | RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4 | GSM8678152 | source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing | RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4 | Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample | whole embryo | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA | GSM8678152 | GSM8678152: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4; Danio rerio; RNA Seq | GSM8678152 r1 | GSM8678152 | 1 | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ELEMENT | Element AVITI | SRP551059 | T_pRfxCas13d_g3Syn_rep4_R1.fastq.gz T_pRfxCas13d_g3Syn_rep4_R2.fastq.gz | fastq fastq | 1372458150.0 | 9149721.0 | GSM8678152 r1 | 0:75 1:75 | A:363668106;C:319963774;G:322725620;T:366049498;N:51152 | 75 | 75 | 363668106 | 319963774 | 322725620 | 366049498 | 51152 | SRX27056956 | SRS23518716 | SRA2032641 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | B | B | biological fallback assumption | element | element | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2024-12-12 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||
| 34367 | 34367 | SRR31695145 | SRX27056955 | SRS23518715 | SRP551059 | PRJNA1197382 | Enhanced RNA targeting CRISPR Cas technology in zebrafish V | GSE284120 | Transcriptome Analysis | Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized | parent bioproject:PRJNA1128082 | pubmed:40091120 | RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3 | GSM8678151 | source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing | RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3 | Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample | whole embryo | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA | GSM8678151 | GSM8678151: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3; Danio rerio; RNA Seq | GSM8678151 r1 | GSM8678151 | 1 | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ELEMENT | Element AVITI | SRP551059 | T_pRfxCas13d_g3Syn_rep3_R1.fastq.gz T_pRfxCas13d_g3Syn_rep3_R2.fastq.gz | fastq fastq | 1716718500.0 | 11444790.0 | GSM8678151 r1 | 0:75 1:75 | A:454308432;C:401470287;G:402968652;T:457908108;N:63021 | 75 | 75 | 454308432 | 401470287 | 402968652 | 457908108 | 63021 | SRX27056955 | SRS23518715 | SRA2032641 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | B | B | biological fallback assumption | element | element | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2024-12-12 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||
| 34368 | 34368 | SRR31695150 | SRX27056954 | SRS23518714 | SRP551059 | PRJNA1197382 | Enhanced RNA targeting CRISPR Cas technology in zebrafish V | GSE284120 | Transcriptome Analysis | Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized | parent bioproject:PRJNA1128082 | pubmed:40091120 | RfxCas13d control rep6 | GSM8678150 | source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing | RfxCas13d control rep6 | Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample | whole embryo | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control | GSM8678150 | GSM8678150: RfxCas13d control rep6; Danio rerio; RNA Seq | GSM8678150 r1 | GSM8678150 | 1 | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ELEMENT | Element AVITI | SRP551059 | T_pRfxCas13d_rep6_R1.fastq.gz T_pRfxCas13d_rep6_R2.fastq.gz | fastq fastq | 1820554200.0 | 12137028.0 | GSM8678150 r1 | 0:75 1:75 | A:480817156;C:426951021;G:428763810;T:483952927;N:69286 | 75 | 75 | 480817156 | 426951021 | 428763810 | 483952927 | 69286 | SRX27056954 | SRS23518714 | SRA2032641 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | B | B | biological fallback assumption | element | element | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2024-12-12 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||
| 34369 | 34369 | SRR31695146 | SRX27056953 | SRS23518713 | SRP551059 | PRJNA1197382 | Enhanced RNA targeting CRISPR Cas technology in zebrafish V | GSE284120 | Transcriptome Analysis | Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized | parent bioproject:PRJNA1128082 | pubmed:40091120 | RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2 | GSM8678149 | source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing | RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2 | Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample | whole embryo | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA | GSM8678149 | GSM8678149: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2; Danio rerio; RNA Seq | GSM8678149 r1 | GSM8678149 | 1 | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ELEMENT | Element AVITI | SRP551059 | T_pRfxCas13d_g1Syn_rep2_R1.fastq.gz T_pRfxCas13d_g1Syn_rep2_R2.fastq.gz | fastq fastq | 1686506550.0 | 11243377.0 | GSM8678149 r1 | 0:75 1:75 | A:445306390;C:395515087;G:396951869;T:448671449;N:61755 | 75 | 75 | 445306390 | 395515087 | 396951869 | 448671449 | 61755 | SRX27056953 | SRS23518713 | SRA2032641 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | B | B | biological fallback assumption | element | element | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2024-12-12 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||
| 34370 | 34370 | SRR31695147 | SRX27056952 | SRS23518712 | SRP551059 | PRJNA1197382 | Enhanced RNA targeting CRISPR Cas technology in zebrafish V | GSE284120 | Transcriptome Analysis | Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized | parent bioproject:PRJNA1128082 | pubmed:40091120 | RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1 | GSM8678148 | source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing | RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1 | Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample | whole embryo | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA | GSM8678148 | GSM8678148: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1; Danio rerio; RNA Seq | GSM8678148 r1 | GSM8678148 | 1 | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ELEMENT | Element AVITI | SRP551059 | T_pRfxCas13d_g1Syn_rep1_R1.fastq.gz T_pRfxCas13d_g1Syn_rep1_R2.fastq.gz | fastq fastq | 2099239050.0 | 13994927.0 | GSM8678148 r1 | 0:75 1:75 | A:555464950;C:490168575;G:492715156;T:560811934;N:78435 | 75 | 75 | 555464950 | 490168575 | 492715156 | 560811934 | 78435 | SRX27056952 | SRS23518712 | SRA2032641 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | B | B | biological fallback assumption | element | element | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2024-12-12 | Blastula | Embryo | Whole Organism | All anatomical structures |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;