run_metadata
1,731 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "bulk" and tissue_curation_coarse = "All anatomical structures"
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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 | |||||||||||
| 25182 | 25182 | SRR25670729 | SRX21396042 | SRS18636200 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA germ ring PAL seq v4 | GSM7716871 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA germ ring PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716871 | GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER | GSM7716871 r1 | GSM7716871 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read2.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read1.fastq.gz | fastq fastq | 2834842912.0 | 9234016.0 | GSM7716871 r1 | 0:52 1:255 | A:725811118;C:702410592;G:747583409;T:651018348;N:8019445 | 52 | 255 | 725811118 | 702410592 | 747583409 | 651018348 | 8019445 | SRX21396042 | SRS18636200 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00023 | 0.30494 | 8e-05 | 0.01793 | 0.99967 | 0.99971 | 0.5 | 1.0 | 52 | 255 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 25183 | 25183 | SRR25670730 | SRX21396042 | SRS18636200 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA germ ring PAL seq v4 | GSM7716871 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA germ ring PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716871 | GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER | GSM7716871 r1 | GSM7716871 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read2.fastq.gz | fastq fastq | 3473033898.0 | 11312814.0 | GSM7716871 r2 | 0:52 1:255 | A:853178471;C:899976159;G:962100712;T:750811461;N:6967095 | 52 | 255 | 853178471 | 899976159 | 962100712 | 750811461 | 6967095 | SRX21396042 | SRS18636200 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00049 | 0.0 | 0.00012 | 0.0 | 0.99941 | 1.0 | 0.64864 | 52 | 255 | T | T | mates < 9% mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||
| 25184 | 25184 | SRR25670731 | SRX21396041 | SRS18636199 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA zfs:0000015 PAL seq v4 | GSM7716870 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA zfs:0000015 PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716870 | GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER | GSM7716870 r1 | GSM7716870 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read2.fastq.gz | fastq fastq | 2695203962.0 | 8779166.0 | GSM7716870 r1 | 0:52 1:255 | A:684535386;C:669852151;G:719008886;T:614209811;N:7597728 | 52 | 255 | 684535386 | 669852151 | 719008886 | 614209811 | 7597728 | SRX21396041 | SRS18636199 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00117 | 0.35837 | 0.00017 | 0.00682 | 0.99859 | 0.99963 | 0.69473 | 1.0 | 52 | 255 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 25185 | 25185 | SRR25670732 | SRX21396041 | SRS18636199 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA zfs:0000015 PAL seq v4 | GSM7716870 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA zfs:0000015 PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716870 | GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER | GSM7716870 r1 | GSM7716870 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read2.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read1.fastq.gz | fastq fastq | 3476338446.0 | 11323578.0 | GSM7716870 r2 | 0:52 1:255 | A:841832234;C:898325199;G:968774318;T:760398070;N:7008625 | 52 | 255 | 841832234 | 898325199 | 968774318 | 760398070 | 7008625 | SRX21396041 | SRS18636199 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00245 | 0.0 | 0.00047 | 0.0 | 0.99803 | 1.0 | 0.58536 | 52 | 255 | T | T | mates < 9% mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||
| 25186 | 25186 | SRR25670733 | SRX21396040 | SRS18636198 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA sphere PAL seq v4 | GSM7716869 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA sphere PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716869 | GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER | GSM7716869 r1 | GSM7716869 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read2.fastq.gz | fastq fastq | 3211687254.0 | 10461522.0 | GSM7716869 r1 | 0:52 1:255 | A:813560400;C:775326762;G:854563477;T:759161458;N:9075157 | 52 | 255 | 813560400 | 775326762 | 854563477 | 759161458 | 9075157 | SRX21396040 | SRS18636198 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00088 | 0.43191 | 0.0004 | 0.01556 | 0.99916 | 0.99961 | 0.55769 | 1.0 | 52 | 255 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 25187 | 25187 | SRR25670734 | SRX21396040 | SRS18636198 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA sphere PAL seq v4 | GSM7716869 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA sphere PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716869 | GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER | GSM7716869 r1 | GSM7716869 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read2.fastq.gz | fastq fastq | 3179916131.0 | 10358033.0 | GSM7716869 r2 | 0:52 1:255 | A:771755667;C:804256300;G:883166175;T:714242073;N:6495916 | 52 | 255 | 771755667 | 804256300 | 883166175 | 714242073 | 6495916 | SRX21396040 | SRS18636198 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00186 | 0.0 | 0.00088 | 0.0 | 0.99862 | 1.0 | 0.64705 | 52 | 255 | T | T | mates < 9% mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||
| 25188 | 25188 | SRR25670735 | SRX21396039 | SRS18636197 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA 1024cell PAL seq v4 | GSM7716868 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA 1024cell PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716868 | GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER | GSM7716868 r1 | GSM7716868 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read2.fastq.gz | fastq fastq | 2191900794.0 | 7139742.0 | GSM7716868 r1 | 0:52 1:255 | A:571954354;C:551162617;G:572445400;T:490238669;N:6099754 | 52 | 255 | 571954354 | 551162617 | 572445400 | 490238669 | 6099754 | SRX21396039 | SRS18636197 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.0011 | 0.43387 | 6e-05 | 0.01058 | 0.99864 | 0.99971 | 0.74576 | 1.0 | 52 | 255 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Zygote | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 25189 | 25189 | SRR25670736 | SRX21396039 | SRS18636197 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA 1024cell PAL seq v4 | GSM7716868 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA 1024cell PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716868 | GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER | GSM7716868 r1 | GSM7716868 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep2_raw_read2.fastq.gz | fastq fastq | 3840723193.0 | 12510499.0 | GSM7716868 r2 | 0:52 1:255 | A:985340216;C:991311706;G:1034487140;T:821820974;N:7763157 | 52 | 255 | 985340216 | 991311706 | 1034487140 | 821820974 | 7763157 | SRX21396039 | SRS18636197 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.0021 | 0.0 | 0.00026 | 0.0 | 0.99859 | 1.0 | 0.71022 | 52 | 255 | T | T | mates < 9% mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Zygote | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||
| 25190 | 25190 | SRR25670737 | SRX21396038 | SRS18636196 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA 128cell PAL seq v4 | GSM7716867 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA 128cell PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716867 | GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER | GSM7716867 r1 | GSM7716867 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read2.fastq.gz | fastq fastq | 2104868443.0 | 6856249.0 | GSM7716867 r1 | 0:52 1:255 | A:539122676;C:505234642;G:558793048;T:495876292;N:5841785 | 52 | 255 | 539122676 | 505234642 | 558793048 | 495876292 | 5841785 | SRX21396038 | SRS18636196 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00035 | 0.29379 | 7e-05 | 0.01129 | 0.99949 | 0.99971 | 0.55882 | 0.79591 | 52 | 255 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 25191 | 25191 | SRR25670738 | SRX21396038 | SRS18636196 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA 128cell PAL seq v4 | GSM7716867 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA 128cell PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716867 | GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER | GSM7716867 r1 | GSM7716867 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read2.fastq.gz | fastq fastq | 3135806371.0 | 10214353.0 | GSM7716867 r2 | 0:52 1:255 | A:776612486;C:774126305;G:853951502;T:724788612;N:6327466 | 52 | 255 | 776612486 | 774126305 | 853951502 | 724788612 | 6327466 | SRX21396038 | SRS18636196 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00066 | 0.0 | 0.00011 | 0.0 | 0.99939 | 1.0 | 0.55737 | 52 | 255 | T | T | mates < 9% mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||
| 25192 | 25192 | SRR25670739 | SRX21396037 | SRS18636195 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA 8cell PAL seq v4 | GSM7716866 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA 8cell PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716866 | GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER | GSM7716866 r1 | GSM7716866 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read2.fastq.gz | fastq fastq | 2618998887.0 | 8530941.0 | GSM7716866 r1 | 0:52 1:255 | A:673066508;C:641446717;G:706546263;T:590452494;N:7486905 | 52 | 255 | 673066508 | 641446717 | 706546263 | 590452494 | 7486905 | SRX21396037 | SRS18636195 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.0009 | 0.43244 | 0.00014 | 0.0054 | 0.99902 | 0.99967 | 0.54901 | 1.0 | 52 | 255 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 25193 | 25193 | SRR25670740 | SRX21396037 | SRS18636195 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA 8cell PAL seq v4 | GSM7716866 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA 8cell PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716866 | GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER | GSM7716866 r1 | GSM7716866 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read2.fastq.gz | fastq fastq | 3028839589.0 | 9865927.0 | GSM7716866 r2 | 0:52 1:255 | A:756368817;C:758868409;G:836949742;T:670545278;N:6107343 | 52 | 255 | 756368817 | 758868409 | 836949742 | 670545278 | 6107343 | SRX21396037 | SRS18636195 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00156 | 0.0 | 0.00026 | 0.0 | 0.99835 | 1.0 | 0.44791 | 52 | 255 | T | T | mates < 9% mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||
| 25194 | 25194 | SRR25670741 | SRX21396036 | SRS18636194 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA 1cell PAL seq v4 | GSM7716865 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA 1cell PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716865 | GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER | GSM7716865 r1 | GSM7716865 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_1cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep1_raw_read2.fastq.gz | fastq fastq | 2050143851.0 | 6677993.0 | GSM7716865 r1 | 0:52 1:255 | A:536391564;C:527126186;G:557802929;T:422990166;N:5833006 | 52 | 255 | 536391564 | 527126186 | 557802929 | 422990166 | 5833006 | SRX21396036 | SRS18636194 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00016 | 0.46479 | 4e-05 | 0.01408 | 0.99979 | 0.99969 | 0.54545 | 1.0 | 52 | 255 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Zygote | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 25195 | 25195 | SRR25670742 | SRX21396036 | SRS18636194 | SRP455680 | PRJNA1006406 | Control of polyA tail length and translation in vertebrate oocytes and early embryos | GSE241107 | Other | During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024. | Fish embryo mRNA 1cell PAL seq v4 | GSM7716865 | source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing | Fish embryo mRNA 1cell PAL seq v4 | For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4 | embryo | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | tissue:embryo|treatment:N1 | GSM7716865 | GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER | GSM7716865 r1 | GSM7716865 | 1 | Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna… | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP455680 | Fish_embryo_mRNA_1cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep2_raw_read2.fastq.gz | fastq fastq | 3406093776.0 | 11094768.0 | GSM7716865 r2 | 0:52 1:255 | A:868054279;C:890446070;G:945289336;T:695324057;N:6980034 | 52 | 255 | 868054279 | 890446070 | 945289336 | 695324057 | 6980034 | SRX21396036 | SRS18636194 | SRA1694849 | Whitehead Institute | Whitehead Institute | 2 | 0.00049 | 0.0 | 0.00014 | 0.0 | 0.99939 | 1.0 | 0.58974 | 52 | 255 | T | T | mates < 9% mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | bulk | bulk | United States | 2023-08-17 | Zygote | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||
| 25273 | 25273 | SRR25764091 | SRX21486763 | SRS18719063 | SRP457108 | PRJNA1009807 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq] | GSE241752 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT bud 10 hpf RNA seq rep2 | GSM7734768 | source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing | WT bud 10 hpf RNA seq rep2 | 3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation | Gastrula | unperturbed growth conditions in E3 medium for zebrafish embryos. | 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. | Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. | strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT | GSM7734768 | GSM7734768: WT bud 10 hpf RNA seq rep2; Danio rerio; RNA Seq | GSM7734768 r1 | GSM7734768 | 1 | 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP457108 | WT_mRNA_bud_2.fastq.gz | fastq | 2470912004.0 | 31168086.0 | GSM7734768 r1 | 0:79.28 | A:656817108;C:568241258;G:504262095;T:741507737;N:83806 | 79 | 656817108 | 568241258 | 504262095 | 741507737 | 83806 | SRX21486763 | SRS18719063 | SRA1700431 | Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.91479 | 0.27298 | 0.74231 | 0.57302 | 79 | B | usable mapping rate | illumina | nextseq | unknown | small_rna | unknown | bulk | bulk | bulk | Germany | 2023-08-28 | Gastrula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 25274 | 25274 | SRR25764092 | SRX21486762 | SRS18719064 | SRP457108 | PRJNA1009807 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq] | GSE241752 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT bud 10 hpf RNA seq rep1 | GSM7734767 | source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing | WT bud 10 hpf RNA seq rep1 | 3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation | Gastrula | unperturbed growth conditions in E3 medium for zebrafish embryos. | 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. | Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. | strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT | GSM7734767 | GSM7734767: WT bud 10 hpf RNA seq rep1; Danio rerio; RNA Seq | GSM7734767 r1 | GSM7734767 | 1 | 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP457108 | WT_mRNA_bud_1.fastq.gz | fastq | 2153494756.0 | 27140032.0 | GSM7734767 r1 | 0:79.35 | A:560793143;C:508962676;G:445126772;T:638539310;N:72855 | 79 | 560793143 | 508962676 | 445126772 | 638539310 | 72855 | SRX21486762 | SRS18719064 | SRA1700431 | Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.88728 | 0.25493 | 0.74369 | 0.56589 | 80 | B | usable mapping rate | illumina | nextseq | unknown | small_rna | unknown | bulk | bulk | bulk | Germany | 2023-08-28 | Gastrula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 25275 | 25275 | SRR25764093 | SRX21486761 | SRS18719061 | SRP457108 | PRJNA1009807 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq] | GSE241752 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT sphere 4 hpf RNA seq rep2 | GSM7734766 | source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing | WT sphere 4 hpf RNA seq rep2 | 3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation | Blastula | unperturbed growth conditions in E3 medium for zebrafish embryos. | 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. | Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. | strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT | GSM7734766 | GSM7734766: WT sphere 4 hpf RNA seq rep2; Danio rerio; RNA Seq | GSM7734766 r1 | GSM7734766 | 1 | 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP457108 | WT_mRNA_sphere_2.fastq.gz | fastq | 2455317157.0 | 30934591.0 | GSM7734766 r1 | 0:79.37 | A:614860604;C:588586084;G:522132289;T:729655621;N:82559 | 79 | 614860604 | 588586084 | 522132289 | 729655621 | 82559 | SRX21486761 | SRS18719061 | SRA1700431 | Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.94124 | 0.10502 | 0.74876 | 0.57752 | 80 | B | usable mapping rate | illumina | nextseq | unknown | small_rna | unknown | bulk | bulk | bulk | Germany | 2023-08-28 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 25276 | 25276 | SRR25764094 | SRX21486760 | SRS18719060 | SRP457108 | PRJNA1009807 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [RNA Seq] | GSE241752 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT sphere 4 hpf RNA seq rep1 | GSM7734765 | source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing | WT sphere 4 hpf RNA seq rep1 | 3’ adapters were trimmed using Trim Galore v0.6.4 with default settings retaining reads of length ≥20. Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterMismatchNmax 1 quantMode TranscriptomeSAM GeneCounts alignEndsType Local seedSearchStartLmax 14 alignIntronMax 10000 outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts. Assembly: GRCz11 Supplementary files format and content: csv; transcripts per million TPM counts per transcript in MANE annotation | Blastula | unperturbed growth conditions in E3 medium for zebrafish embryos. | 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. | Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. | strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT | GSM7734765 | GSM7734765: WT sphere 4 hpf RNA seq rep1; Danio rerio; RNA Seq | GSM7734765 r1 | GSM7734765 | 1 | 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. 250 ng of the same total RNA used for mim tRNAseq library preparation were used for mRNA Seq library construction with the Zymo Seq RiboFree Total RNA Library Kit Zymo Research #R3000. Libraries were sequenced on a NextSeq 500 platform. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP457108 | WT_mRNA_sphere_1.fastq.gz | fastq | 2399640874.0 | 30232118.0 | GSM7734765 r1 | 0:79.37 | A:589069860;C:593745131;G:511439690;T:705305674;N:80519 | 79 | 589069860 | 593745131 | 511439690 | 705305674 | 80519 | SRX21486760 | SRS18719060 | SRA1700431 | Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.85882 | 0.11848 | 0.75122 | 0.5883 | 80 | B | usable mapping rate | illumina | nextseq | unknown | small_rna | unknown | bulk | bulk | bulk | Germany | 2023-08-28 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28113 | 28113 | SRR26209648 | SRX21920662 | SRS19005181 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 3 | GSM7812991 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812991 | GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq | GSM7812991 r1 | GSM7812991 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A30_S48_L005_R1_001.fastq.gz | fastq | 616449359.0 | 6103459.0 | GSM7812991 r1 | 0:101 | A:152808626;C:149738763;G:141639387;T:172257280;N:5303 | 101 | 152808626 | 149738763 | 141639387 | 172257280 | 5303 | SRX21920662 | SRS19005181 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94246 | 0.08766 | 0.69443 | 0.4842 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28114 | 28114 | SRR26209649 | SRX21920662 | SRS19005181 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 3 | GSM7812991 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812991 | GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq | GSM7812991 r1 | GSM7812991 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A30_S48_L006_R1_001.fastq.gz | fastq | 609999297.0 | 6039597.0 | GSM7812991 r2 | 0:101 | A:151226657;C:148143193;G:140088806;T:170530812;N:9829 | 101 | 151226657 | 148143193 | 140088806 | 170530812 | 9829 | SRX21920662 | SRS19005181 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94201 | 0.08569 | 0.69572 | 0.48692 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28115 | 28115 | SRR26209650 | SRX21920662 | SRS19005181 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 3 | GSM7812991 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812991 | GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq | GSM7812991 r1 | GSM7812991 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A30_S48_L007_R1_001.fastq.gz | fastq | 543730470.0 | 5383470.0 | GSM7812991 r3 | 0:101 | A:134685766;C:132190291;G:124881864;T:151967639;N:4910 | 101 | 134685766 | 132190291 | 124881864 | 151967639 | 4910 | SRX21920662 | SRS19005181 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.9431 | 0.08733 | 0.69524 | 0.48528 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28116 | 28116 | SRR26209651 | SRX21920662 | SRS19005181 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 3 | GSM7812991 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812991 | GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq | GSM7812991 r1 | GSM7812991 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A30_S16_L007_R1_001.fastq.gz | fastq | 649354149.0 | 6429249.0 | GSM7812991 r4 | 0:101 | A:160756303;C:158145998;G:149623680;T:180816390;N:11778 | 101 | 160756303 | 158145998 | 149623680 | 180816390 | 11778 | SRX21920662 | SRS19005181 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94438 | 0.08618 | 0.69473 | 0.48809 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28117 | 28117 | SRR26209752 | SRX21920662 | SRS19005181 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 3 | GSM7812991 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812991 | GSM7812991: unDMSO t1 WT 3; Danio rerio; RNA Seq | GSM7812991 r1 | GSM7812991 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A30_S16_L008_R1_001.fastq.gz | fastq | 650450504.0 | 6440104.0 | GSM7812991 r5 | 0:101 | A:161054597;C:158340761;G:149784923;T:181251361;N:18862 | 101 | 161054597 | 158340761 | 149784923 | 181251361 | 18862 | SRX21920662 | SRS19005181 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94338 | 0.08713 | 0.6968 | 0.48443 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28118 | 28118 | SRR26209652 | SRX21920661 | SRS19005180 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 2 | GSM7812990 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812990 | GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq | GSM7812990 r1 | GSM7812990 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A29_S46_L005_R1_001.fastq.gz | fastq | 593068162.0 | 5871962.0 | GSM7812990 r1 | 0:101 | A:147906639;C:143944406;G:137307101;T:163904929;N:5087 | 101 | 147906639 | 143944406 | 137307101 | 163904929 | 5087 | SRX21920661 | SRS19005180 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94371 | 0.06473 | 0.69378 | 0.47765 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28119 | 28119 | SRR26209653 | SRX21920661 | SRS19005180 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 2 | GSM7812990 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812990 | GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq | GSM7812990 r1 | GSM7812990 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A29_S46_L006_R1_001.fastq.gz | fastq | 588323081.0 | 5824981.0 | GSM7812990 r2 | 0:101 | A:146630863;C:142829925;G:136124185;T:162728186;N:9922 | 101 | 146630863 | 142829925 | 136124185 | 162728186 | 9922 | SRX21920661 | SRS19005180 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94282 | 0.06357 | 0.69418 | 0.47665 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28120 | 28120 | SRR26209654 | SRX21920661 | SRS19005180 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 2 | GSM7812990 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812990 | GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq | GSM7812990 r1 | GSM7812990 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A29_S46_L007_R1_001.fastq.gz | fastq | 521265747.0 | 5161047.0 | GSM7812990 r3 | 0:101 | A:129905878;C:126622019;G:120526207;T:144206853;N:4790 | 101 | 129905878 | 126622019 | 120526207 | 144206853 | 4790 | SRX21920661 | SRS19005180 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94508 | 0.06499 | 0.69367 | 0.4834 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28121 | 28121 | SRR26209655 | SRX21920661 | SRS19005180 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 2 | GSM7812990 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812990 | GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq | GSM7812990 r1 | GSM7812990 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A29_S26_L007_R1_001.fastq.gz | fastq | 623834580.0 | 6176580.0 | GSM7812990 r4 | 0:101 | A:155642981;C:151651242;G:144681951;T:171847192;N:11214 | 101 | 155642981 | 151651242 | 144681951 | 171847192 | 11214 | SRX21920661 | SRS19005180 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94531 | 0.06514 | 0.69225 | 0.48187 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28122 | 28122 | SRR26209656 | SRX21920661 | SRS19005180 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 2 | GSM7812990 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812990 | GSM7812990: unDMSO t1 WT 2; Danio rerio; RNA Seq | GSM7812990 r1 | GSM7812990 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A29_S26_L008_R1_001.fastq.gz | fastq | 622155960.0 | 6159960.0 | GSM7812990 r5 | 0:101 | A:155145221;C:151231599;G:144290581;T:171470641;N:17918 | 101 | 155145221 | 151231599 | 144290581 | 171470641 | 17918 | SRX21920661 | SRS19005180 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94319 | 0.06413 | 0.69449 | 0.48159 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28123 | 28123 | SRR26209657 | SRX21920660 | SRS19005179 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 1 | GSM7812989 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812989 | GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq | GSM7812989 r1 | GSM7812989 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A28_S45_L005_R1_001.fastq.gz | fastq | 602520550.0 | 5965550.0 | GSM7812989 r1 | 0:101 | A:149619230;C:146559346;G:139674646;T:166662143;N:5185 | 101 | 149619230 | 146559346 | 139674646 | 166662143 | 5185 | SRX21920660 | SRS19005179 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94449 | 0.06296 | 0.69487 | 0.48 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28124 | 28124 | SRR26209658 | SRX21920660 | SRS19005179 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 1 | GSM7812989 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812989 | GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq | GSM7812989 r1 | GSM7812989 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A28_S45_L006_R1_001.fastq.gz | fastq | 596942522.0 | 5910322.0 | GSM7812989 r2 | 0:101 | A:148193962;C:145221539;G:138267073;T:165249833;N:10115 | 101 | 148193962 | 145221539 | 138267073 | 165249833 | 10115 | SRX21920660 | SRS19005179 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.9446 | 0.06327 | 0.69562 | 0.48183 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28125 | 28125 | SRR26209659 | SRX21920660 | SRS19005179 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 1 | GSM7812989 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812989 | GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq | GSM7812989 r1 | GSM7812989 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A28_S45_L007_R1_001.fastq.gz | fastq | 532539064.0 | 5272664.0 | GSM7812989 r3 | 0:101 | A:132217323;C:129660296;G:123303893;T:147352732;N:4820 | 101 | 132217323 | 129660296 | 123303893 | 147352732 | 4820 | SRX21920660 | SRS19005179 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94579 | 0.06237 | 0.69554 | 0.46658 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28126 | 28126 | SRR26209660 | SRX21920660 | SRS19005179 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 1 | GSM7812989 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812989 | GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq | GSM7812989 r1 | GSM7812989 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A28_S29_L007_R1_001.fastq.gz | fastq | 633337569.0 | 6270669.0 | GSM7812989 r4 | 0:101 | A:157286526;C:154336036;G:147137950;T:174565295;N:11762 | 101 | 157286526 | 154336036 | 147137950 | 174565295 | 11762 | SRX21920660 | SRS19005179 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94562 | 0.06294 | 0.69489 | 0.47406 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28127 | 28127 | SRR26209661 | SRX21920660 | SRS19005179 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 WT 1 | GSM7812989 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 WT 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:WT|treatment:unDMSO | GSM7812989 | GSM7812989: unDMSO t1 WT 1; Danio rerio; RNA Seq | GSM7812989 r1 | GSM7812989 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A28_S29_L008_R1_001.fastq.gz | fastq | 636051540.0 | 6297540.0 | GSM7812989 r5 | 0:101 | A:157845668;C:154972063;G:147765532;T:175449801;N:18476 | 101 | 157845668 | 154972063 | 147765532 | 175449801 | 18476 | SRX21920660 | SRS19005179 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.9471 | 0.06288 | 0.69536 | 0.4797 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28128 | 28128 | SRR26209662 | SRX21920659 | SRS19005178 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 3 | GSM7812988 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812988 | GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq | GSM7812988 r1 | GSM7812988 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A36_S54_L005_R1_001.fastq.gz | fastq | 674188635.0 | 6675135.0 | GSM7812988 r1 | 0:101 | A:173104307;C:161481671;G:152542615;T:187053812;N:6230 | 101 | 173104307 | 161481671 | 152542615 | 187053812 | 6230 | SRX21920659 | SRS19005178 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94039 | 0.07795 | 0.69877 | 0.48386 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28129 | 28129 | SRR26209663 | SRX21920659 | SRS19005178 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 3 | GSM7812988 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812988 | GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq | GSM7812988 r1 | GSM7812988 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A36_S54_L006_R1_001.fastq.gz | fastq | 667048339.0 | 6604439.0 | GSM7812988 r2 | 0:101 | A:171316049;C:159786547;G:150743446;T:185190228;N:12069 | 101 | 171316049 | 159786547 | 150743446 | 185190228 | 12069 | SRX21920659 | SRS19005178 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94064 | 0.07881 | 0.69767 | 0.48162 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28130 | 28130 | SRR26209664 | SRX21920659 | SRS19005178 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 3 | GSM7812988 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812988 | GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq | GSM7812988 r1 | GSM7812988 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A36_S54_L007_R1_001.fastq.gz | fastq | 596645683.0 | 5907383.0 | GSM7812988 r3 | 0:101 | A:153131508;C:143126741;G:134745614;T:165635953;N:5867 | 101 | 153131508 | 143126741 | 134745614 | 165635953 | 5867 | SRX21920659 | SRS19005178 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94156 | 0.07795 | 0.69751 | 0.4833 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28131 | 28131 | SRR26209665 | SRX21920659 | SRS19005178 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 3 | GSM7812988 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812988 | GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq | GSM7812988 r1 | GSM7812988 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A36_S12_L007_R1_001.fastq.gz | fastq | 712385926.0 | 7053326.0 | GSM7812988 r4 | 0:101 | A:183100436;C:171026605;G:161510527;T:196734608;N:13750 | 101 | 183100436 | 171026605 | 161510527 | 196734608 | 13750 | SRX21920659 | SRS19005178 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94298 | 0.07892 | 0.6997 | 0.48331 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28132 | 28132 | SRR26209666 | SRX21920659 | SRS19005178 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 3 | GSM7812988 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812988 | GSM7812988: unDMSO t1 K2 3; Danio rerio; RNA Seq | GSM7812988 r1 | GSM7812988 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A36_S12_L008_R1_001.fastq.gz | fastq | 714661355.0 | 7075855.0 | GSM7812988 r5 | 0:101 | A:183454698;C:171554090;G:162064705;T:197567065;N:20797 | 101 | 183454698 | 171554090 | 162064705 | 197567065 | 20797 | SRX21920659 | SRS19005178 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94316 | 0.07877 | 0.70051 | 0.48354 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28133 | 28133 | SRR26209667 | SRX21920658 | SRS19005177 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 2 | GSM7812987 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812987 | GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq | GSM7812987 r1 | GSM7812987 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A35_S53_L005_R1_001.fastq.gz | fastq | 611900723.0 | 6058423.0 | GSM7812987 r1 | 0:101 | A:154668392;C:147817141;G:139653400;T:169756342;N:5448 | 101 | 154668392 | 147817141 | 139653400 | 169756342 | 5448 | SRX21920658 | SRS19005177 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94636 | 0.08022 | 0.69962 | 0.48201 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28134 | 28134 | SRR26209668 | SRX21920658 | SRS19005177 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 2 | GSM7812987 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812987 | GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq | GSM7812987 r1 | GSM7812987 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A35_S53_L006_R1_001.fastq.gz | fastq | 602971818.0 | 5970018.0 | GSM7812987 r2 | 0:101 | A:152346877;C:145640105;G:137576284;T:167398281;N:10271 | 101 | 152346877 | 145640105 | 137576284 | 167398281 | 10271 | SRX21920658 | SRS19005177 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94549 | 0.08086 | 0.69781 | 0.47842 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28135 | 28135 | SRR26209669 | SRX21920658 | SRS19005177 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 2 | GSM7812987 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812987 | GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq | GSM7812987 r1 | GSM7812987 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A35_S53_L007_R1_001.fastq.gz | fastq | 539246575.0 | 5339075.0 | GSM7812987 r3 | 0:101 | A:136317506;C:130390122;G:122927887;T:149606028;N:5032 | 101 | 136317506 | 130390122 | 122927887 | 149606028 | 5032 | SRX21920658 | SRS19005177 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94653 | 0.08075 | 0.69704 | 0.48374 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28136 | 28136 | SRR26209670 | SRX21920658 | SRS19005177 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 2 | GSM7812987 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812987 | GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq | GSM7812987 r1 | GSM7812987 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A35_S47_L007_R1_001.fastq.gz | fastq | 643197593.0 | 6368293.0 | GSM7812987 r4 | 0:101 | A:162743675;C:155711536;G:147135700;T:177594459;N:12223 | 101 | 162743675 | 155711536 | 147135700 | 177594459 | 12223 | SRX21920658 | SRS19005177 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94757 | 0.08023 | 0.70055 | 0.48458 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28137 | 28137 | SRR26209671 | SRX21920658 | SRS19005177 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 2 | GSM7812987 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812987 | GSM7812987: unDMSO t1 K2 2; Danio rerio; RNA Seq | GSM7812987 r1 | GSM7812987 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A35_S47_L008_R1_001.fastq.gz | fastq | 644356063.0 | 6379763.0 | GSM7812987 r5 | 0:101 | A:162915651;C:155935181;G:147406641;T:178079118;N:19472 | 101 | 162915651 | 155935181 | 147406641 | 178079118 | 19472 | SRX21920658 | SRS19005177 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94817 | 0.08218 | 0.70017 | 0.48286 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28138 | 28138 | SRR26209672 | SRX21920657 | SRS19005176 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 1 | GSM7812986 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812986 | GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq | GSM7812986 r1 | GSM7812986 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A34_S52_L005_R1_001.fastq.gz | fastq | 615996374.0 | 6098974.0 | GSM7812986 r1 | 0:101 | A:156934542;C:147417998;G:139301915;T:172336421;N:5498 | 101 | 156934542 | 147417998 | 139301915 | 172336421 | 5498 | SRX21920657 | SRS19005176 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94179 | 0.07628 | 0.69512 | 0.48041 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28139 | 28139 | SRR26209673 | SRX21920657 | SRS19005176 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 1 | GSM7812986 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812986 | GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq | GSM7812986 r1 | GSM7812986 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A34_S52_L006_R1_001.fastq.gz | fastq | 608875571.0 | 6028471.0 | GSM7812986 r2 | 0:101 | A:155127967;C:145701864;G:137575885;T:170459017;N:10838 | 101 | 155127967 | 145701864 | 137575885 | 170459017 | 10838 | SRX21920657 | SRS19005176 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94248 | 0.07563 | 0.69512 | 0.47982 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28140 | 28140 | SRR26209674 | SRX21920657 | SRS19005176 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 1 | GSM7812986 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812986 | GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq | GSM7812986 r1 | GSM7812986 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A34_S52_L007_R1_001.fastq.gz | fastq | 539739455.0 | 5343955.0 | GSM7812986 r3 | 0:101 | A:137431217;C:129328124;G:121891472;T:151083373;N:5269 | 101 | 137431217 | 129328124 | 121891472 | 151083373 | 5269 | SRX21920657 | SRS19005176 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.9438 | 0.07511 | 0.69654 | 0.48083 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28141 | 28141 | SRR26209675 | SRX21920657 | SRS19005176 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 1 | GSM7812986 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812986 | GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq | GSM7812986 r1 | GSM7812986 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A34_S65_L007_R1_001.fastq.gz | fastq | 648984489.0 | 6425589.0 | GSM7812986 r4 | 0:101 | A:165552674;C:155580501;G:147078092;T:180761105;N:12117 | 101 | 165552674 | 155580501 | 147078092 | 180761105 | 12117 | SRX21920657 | SRS19005176 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94513 | 0.07694 | 0.69451 | 0.48174 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28142 | 28142 | SRR26209676 | SRX21920657 | SRS19005176 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K2 1 | GSM7812986 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K2 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K2|treatment:unDMSO | GSM7812986 | GSM7812986: unDMSO t1 K2 1; Danio rerio; RNA Seq | GSM7812986 r1 | GSM7812986 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A34_S65_L008_R1_001.fastq.gz | fastq | 651988330.0 | 6455330.0 | GSM7812986 r5 | 0:101 | A:166130853;C:156282200;G:147738788;T:181817695;N:18794 | 101 | 166130853 | 156282200 | 147738788 | 181817695 | 18794 | SRX21920657 | SRS19005176 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94437 | 0.0759 | 0.69597 | 0.48083 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28143 | 28143 | SRR26209677 | SRX21920656 | SRS19005175 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 3 | GSM7812985 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812985 | GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq | GSM7812985 r1 | GSM7812985 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A33_S51_L005_R1_001.fastq.gz | fastq | 621669544.0 | 6155144.0 | GSM7812985 r1 | 0:101 | A:157346917;C:148083763;G:141122336;T:175110946;N:5582 | 101 | 157346917 | 148083763 | 141122336 | 175110946 | 5582 | SRX21920656 | SRS19005175 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94207 | 0.06859 | 0.69473 | 0.48838 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28144 | 28144 | SRR26209678 | SRX21920656 | SRS19005175 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 3 | GSM7812985 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812985 | GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq | GSM7812985 r1 | GSM7812985 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A33_S51_L006_R1_001.fastq.gz | fastq | 613437842.0 | 6073642.0 | GSM7812985 r2 | 0:101 | A:155200714;C:146135271;G:139223090;T:172868018;N:10749 | 101 | 155200714 | 146135271 | 139223090 | 172868018 | 10749 | SRX21920656 | SRS19005175 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94144 | 0.06885 | 0.69471 | 0.48996 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28145 | 28145 | SRR26209679 | SRX21920656 | SRS19005175 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 3 | GSM7812985 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812985 | GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq | GSM7812985 r1 | GSM7812985 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A33_S51_L007_R1_001.fastq.gz | fastq | 546684518.0 | 5412718.0 | GSM7812985 r3 | 0:101 | A:138292090;C:130364936;G:123978492;T:154043685;N:5315 | 101 | 138292090 | 130364936 | 123978492 | 154043685 | 5315 | SRX21920656 | SRS19005175 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94375 | 0.06988 | 0.69589 | 0.48741 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28146 | 28146 | SRR26209680 | SRX21920656 | SRS19005175 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 3 | GSM7812985 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812985 | GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq | GSM7812985 r1 | GSM7812985 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A33_S43_L007_R1_001.fastq.gz | fastq | 651065089.0 | 6446189.0 | GSM7812985 r4 | 0:101 | A:164874330;C:155389435;G:148130531;T:182658473;N:12320 | 101 | 164874330 | 155389435 | 148130531 | 182658473 | 12320 | SRX21920656 | SRS19005175 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94247 | 0.06954 | 0.69538 | 0.48283 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28147 | 28147 | SRR26209681 | SRX21920656 | SRS19005175 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 3 | GSM7812985 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 3 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812985 | GSM7812985: unDMSO t1 K1 3; Danio rerio; RNA Seq | GSM7812985 r1 | GSM7812985 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A33_S43_L008_R1_001.fastq.gz | fastq | 652838952.0 | 6463752.0 | GSM7812985 r5 | 0:101 | A:165235507;C:155756581;G:148483290;T:183344035;N:19539 | 101 | 165235507 | 155756581 | 148483290 | 183344035 | 19539 | SRX21920656 | SRS19005175 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94297 | 0.06917 | 0.69593 | 0.4827 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28148 | 28148 | SRR26209682 | SRX21920655 | SRS19005174 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 2 | GSM7812984 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812984 | GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq | GSM7812984 r1 | GSM7812984 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A32_S50_L005_R1_001.fastq.gz | fastq | 531938215.0 | 5266715.0 | GSM7812984 r1 | 0:101 | A:131083905;C:128715617;G:122601298;T:149532970;N:4425 | 101 | 131083905 | 128715617 | 122601298 | 149532970 | 4425 | SRX21920655 | SRS19005174 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94249 | 0.07108 | 0.69485 | 0.47386 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28149 | 28149 | SRR26209683 | SRX21920655 | SRS19005174 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 2 | GSM7812984 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812984 | GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq | GSM7812984 r1 | GSM7812984 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A32_S50_L006_R1_001.fastq.gz | fastq | 527781863.0 | 5225563.0 | GSM7812984 r2 | 0:101 | A:130119726;C:127646784;G:121549831;T:148456993;N:8529 | 101 | 130119726 | 127646784 | 121549831 | 148456993 | 8529 | SRX21920655 | SRS19005174 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94199 | 0.0713 | 0.69337 | 0.473 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28150 | 28150 | SRR26209684 | SRX21920655 | SRS19005174 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 2 | GSM7812984 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812984 | GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq | GSM7812984 r1 | GSM7812984 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A32_S50_L007_R1_001.fastq.gz | fastq | 472785040.0 | 4681040.0 | GSM7812984 r3 | 0:101 | A:116503463;C:114489771;G:108989839;T:132797698;N:4269 | 101 | 116503463 | 114489771 | 108989839 | 132797698 | 4269 | SRX21920655 | SRS19005174 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94373 | 0.07285 | 0.69467 | 0.47913 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28151 | 28151 | SRR26209685 | SRX21920655 | SRS19005174 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 2 | GSM7812984 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812984 | GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq | GSM7812984 r1 | GSM7812984 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A32_S71_L007_R1_001.fastq.gz | fastq | 561056414.0 | 5555014.0 | GSM7812984 r4 | 0:101 | A:138240115;C:136040813;G:129592563;T:157172399;N:10524 | 101 | 138240115 | 136040813 | 129592563 | 157172399 | 10524 | SRX21920655 | SRS19005174 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94357 | 0.07109 | 0.69544 | 0.47169 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28152 | 28152 | SRR26209686 | SRX21920655 | SRS19005174 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 2 | GSM7812984 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 2 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812984 | GSM7812984: unDMSO t1 K1 2; Danio rerio; RNA Seq | GSM7812984 r1 | GSM7812984 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A32_S71_L008_R1_001.fastq.gz | fastq | 563109744.0 | 5575344.0 | GSM7812984 r5 | 0:101 | A:138778764;C:136444809;G:129964766;T:157904708;N:16697 | 101 | 138778764 | 136444809 | 129964766 | 157904708 | 16697 | SRX21920655 | SRS19005174 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94358 | 0.07253 | 0.69345 | 0.47443 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28153 | 28153 | SRR26209687 | SRX21920654 | SRS19005173 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 1 | GSM7812983 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812983 | GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq | GSM7812983 r1 | GSM7812983 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A31_S49_L005_R1_001.fastq.gz | fastq | 576725857.0 | 5710157.0 | GSM7812983 r1 | 0:101 | A:142557020;C:140092748;G:133378036;T:160693137;N:4916 | 101 | 142557020 | 140092748 | 133378036 | 160693137 | 4916 | SRX21920654 | SRS19005173 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94239 | 0.07259 | 0.69398 | 0.47675 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28154 | 28154 | SRR26209688 | SRX21920654 | SRS19005173 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 1 | GSM7812983 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812983 | GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq | GSM7812983 r1 | GSM7812983 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A31_S49_L006_R1_001.fastq.gz | fastq | 569166310.0 | 5635310.0 | GSM7812983 r2 | 0:101 | A:140702145;C:138232540;G:131558917;T:158663414;N:9294 | 101 | 140702145 | 138232540 | 131558917 | 158663414 | 9294 | SRX21920654 | SRS19005173 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94221 | 0.07252 | 0.69524 | 0.4833 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28155 | 28155 | SRR26209689 | SRX21920654 | SRS19005173 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 1 | GSM7812983 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812983 | GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq | GSM7812983 r1 | GSM7812983 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A31_S49_L007_R1_001.fastq.gz | fastq | 505699425.0 | 5006925.0 | GSM7812983 r3 | 0:101 | A:124940125;C:122891114;G:116919354;T:140944307;N:4525 | 101 | 124940125 | 122891114 | 116919354 | 140944307 | 4525 | SRX21920654 | SRS19005173 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.944 | 0.07242 | 0.69473 | 0.48289 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||
| 28156 | 28156 | SRR26209690 | SRX21920654 | SRS19005173 | SRP463749 | PRJNA1022096 | Zebrafish reveal new roles for Fam83f in hatching and DNA damage mediated autophagic responses | GSE244291 | Transcriptome Analysis | The FAM83 Family with sequence similarity 83 family is highly conserved in vertebrates yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development and here we report the generation of fam83f knock out fam83f / zebrafish which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatch gland of developing zebrafish embryos and that fam83f / embryos hatch earlier than WT counterparts despite developing at a comparable temporal rate. We demonstrate that fam83f / embryos are more sensitive to ionizing radiation than WT embryos a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol 3 phosphate PI3P binding proteins and impairment of cellular degradation pathways particularly autophagy which is a crucial component of the DNA damage response. Finally we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo. Overall design: fam83fa / zebrafish are more sensitive to ionizing radiation IR than WT counterparts. We conducted bulk RNA seq on WT vs two different fam83fa / K1 and K2 zebrafish lines by subjecting 24 hpf embryos from each genotype to IR th… | pubmed:39437839 | unDMSO t1 K1 1 | GSM7812983 | source name:whole embryo|tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO|geo loc name:missing|collection date:missing | unDMSO t1 K1 1 | Cutadapt 1.9.1 rsem 1.3.0 star 2.5.2a Assembly: GRCz11 assembly Supplementary files format and content: *.genes.results are rsem count files | whole embryo | Embryos were exposed to gamma IR of 20 Gy at xxx hpf | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | Zebrafish embryos post collection were maintained at 28.5C in E2 medium at a density ⋜ 50 embryos | tissue:whole embryo|timepoint:t1|genotype:K1|treatment:unDMSO | GSM7812983 | GSM7812983: unDMSO t1 K1 1; Danio rerio; RNA Seq | GSM7812983 r1 | GSM7812983 | 1 | Total RNA was extracted using RNeasy Mini Kit QIAGEN rRNA depletion Rio Zero Plus rRNA Depletion Kit Ilumina then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP463749 | loader:fastq load.py | JON686A31_S27_L007_R1_001.fastq.gz | fastq | 598624374.0 | 5926974.0 | GSM7812983 r4 | 0:101 | A:147863525;C:145723385;G:138724140;T:166302217;N:11107 | 101 | 147863525 | 145723385 | 138724140 | 166302217 | 11107 | SRX21920654 | SRS19005173 | SRA1722794 | Devenport, Molecular Biology, Princeton University | Devenport, Molecular Biology, Princeton University | 1 | 0.94426 | 0.07312 | 0.69479 | 0.48056 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United States | 2023-09-28 | Undetermined | 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");;