run_metadata
140 rows where experiment.platform = "ILLUMINA", technology = "bulk" and tissue_curation_coarse = "Multi-system"
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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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| 9702 | 9702 | ERR3301003 | ERX3327070 | ERS3389658 | 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: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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 th… | WT heart rep 3 | SAMEA5585434 | 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:SAMEA5585434|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 heart rep 3|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:6|organism part:heart|sample name:E MTAB 7920:WT heart rep 3|scientific name:Danio rerio|sex:female|strain:AB | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:WT heart rep 3 p | WT heart rep 3 p | RNA seq of zebrafish sa12692 mutants against WT controls | Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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. T… | Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart | 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_lane1WTheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_2.fq.gz | fastq fastq | 7339830080.0 | 45873938.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart3 | 0:80 1:80 | A:1985328994;C:1673818891;G:1695753386;T:1984031668;N:897141 | 80 | 80 | 1985328994 | 1673818891 | 1695753386 | 1984031668 | 897141 | ERX3327070 | ERS3389658 | 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 | 0.9311 | 0.94858 | 0.07774 | 0.07789 | 0.76378 | 0.76394 | 0.52815 | 0.52065 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 9703 | 9703 | ERR3301002 | ERX3327069 | ERS3389657 | 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: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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 th… | WT heart rep 2 | SAMEA5585433 | 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:SAMEA5585433|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 heart rep 2|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:5|organism part:heart|sample name:E MTAB 7920:WT heart rep 2|scientific name:Danio rerio|sex:female|strain:AB | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:WT heart rep 2 p | WT heart rep 2 p | RNA seq of zebrafish sa12692 mutants against WT controls | Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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. T… | Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart | 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_lane1WTheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_2.fq.gz | fastq fastq | 7486415840.0 | 46790099.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart2 | 0:80 1:80 | A:2020798219;C:1702752807;G:1731176796;T:2030756525;N:931493 | 80 | 80 | 2020798219 | 1702752807 | 1731176796 | 2030756525 | 931493 | ERX3327069 | ERS3389657 | 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 | 0.93397 | 0.9509 | 0.07752 | 0.07859 | 0.76019 | 0.76002 | 0.54034 | 0.54728 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 9704 | 9704 | ERR3301001 | ERX3327068 | ERS3389656 | 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: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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 th… | WT heart rep 1 | SAMEA5585432 | 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:SAMEA5585432|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 heart rep 1|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:4|organism part:heart|sample name:E MTAB 7920:WT heart rep 1|scientific name:Danio rerio|sex:female|strain:AB | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:WT heart rep 1 p | WT heart rep 1 p | RNA seq of zebrafish sa12692 mutants against WT controls | Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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. T… | Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart | 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_lane1WTheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_2.fq.gz | fastq fastq | 6814600800.0 | 42591255.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart1 | 0:80 1:80 | A:1823108307;C:1567497576;G:1587567005;T:1835589927;N:837985 | 80 | 80 | 1823108307 | 1567497576 | 1587567005 | 1835589927 | 837985 | ERX3327068 | ERS3389656 | 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 | 0.93109 | 0.94806 | 0.07581 | 0.07635 | 0.75907 | 0.75988 | 0.54746 | 0.54753 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 9708 | 9708 | ERR3300997 | ERX3327064 | ERS3389652 | 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: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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 th… | Mutant heart rep 3 | SAMEA5585428 | 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:SAMEA5585428|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 heart rep 3|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:3|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 3|scientific name:Danio rerio|sex:female|strain:sa12692 mutant | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:Mutant heart rep 3 p | Mutant heart rep 3 p | RNA seq of zebrafish sa12692 mutants against WT controls | Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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. T… | Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart | 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_lane1Mutantheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_2.fq.gz | fastq fastq | 7240447520.0 | 45252797.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart3 | 0:80 1:80 | A:1968283412;C:1645458614;G:1652590010;T:1973242527;N:872957 | 80 | 80 | 1968283412 | 1645458614 | 1652590010 | 1973242527 | 872957 | ERX3327064 | ERS3389652 | 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 | 0.92784 | 0.94597 | 0.08601 | 0.08686 | 0.76702 | 0.76449 | 0.50929 | 0.52685 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 9709 | 9709 | ERR3300996 | ERX3327063 | ERS3389651 | 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: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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 th… | Mutant heart rep 2 | SAMEA5585427 | 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:SAMEA5585427|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 heart rep 2|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:2|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 2|scientific name:Danio rerio|sex:female|strain:sa12692 mutant | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:Mutant heart rep 2 p | Mutant heart rep 2 p | RNA seq of zebrafish sa12692 mutants against WT controls | Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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. T… | Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart | 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_lane1Mutantheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_2.fq.gz | fastq fastq | 7347029600.0 | 45918935.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart2 | 0:80 1:80 | A:1967915665;C:1690507331;G:1712776156;T:1974918219;N:912229 | 80 | 80 | 1967915665 | 1690507331 | 1712776156 | 1974918219 | 912229 | ERX3327063 | ERS3389651 | 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 | 0.93337 | 0.94978 | 0.07673 | 0.07724 | 0.76755 | 0.76798 | 0.53415 | 0.51157 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 9710 | 9710 | ERR3300995 | ERX3327062 | ERS3389650 | 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: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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 th… | Mutant heart rep 1 | SAMEA5585426 | Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway | ENA FIRST PUBLIC:2021 04 30T00:25:02Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585426|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 30T00:25:02Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 1|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:1|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 1|scientific name:Danio rerio|sex:female|strain:sa12692 mutant | NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls | E MTAB 7920:Mutant heart rep 1 p | Mutant heart rep 1 p | RNA seq of zebrafish sa12692 mutants against WT controls | Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. 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. T… | Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart | 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_lane1Mutantheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_2.fq.gz | fastq fastq | 6296502880.0 | 39353143.0 | E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart1 | 0:80 1:80 | A:1677737687;C:1460767489;G:1468915029;T:1688319734;N:762941 | 80 | 80 | 1677737687 | 1460767489 | 1468915029 | 1688319734 | 762941 | ERX3327062 | ERS3389650 | 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 | 0.93775 | 0.9516 | 0.07994 | 0.08077 | 0.75844 | 0.75759 | 0.51937 | 0.52207 | 80 | 80 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | trueseq | bulk | bulk | bulk | Ireland | 2019-04-30 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 9812 | 9812 | ERR3931362 | ERX3938952 | ERS4329529 | ERP120057 | PRJEB36819 | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E-MTAB-8800 | Transcriptome Analysis | Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | WKM 7 ED | SAMEA6565186 | Institute of Molecular Genetics of the Czech Academy of Sciences | ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565186|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 ED | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E MTAB 8800:WKM 7 ED s | WKM 7 ED s | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | Experimental Factor: stimulus:n1 | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | SINGLE | ILLUMINA | NextSeq 500 | ERP120057 | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | 10_WKM_7_ED.fastq.gz | fastq | 3603783627.0 | 47724788.0 | E MTAB 8800:WKM 7 ED | 0:75.51 1:0 | A:730277817;C:1059558661;G:1006087781;T:807771859;N:87509 | 75 | 0 | 730277817 | 1059558661 | 1006087781 | 807771859 | 87509 | ERX3938952 | ERS4329529 | ERA2383450 | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | 1 | 0.96114 | 0.20335 | 0.83798 | 0.76524 | 76 | B | usable mapping rate | illumina | nextseq | full_length | rrna_depletion | smarter | bulk | bulk | bulk | Czech Republic | 2021-12-31 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||
| 9813 | 9813 | ERR3931361 | ERX3938951 | ERS4329528 | ERP120057 | PRJEB36819 | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E-MTAB-8800 | Transcriptome Analysis | Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | WKM 7 EaD | SAMEA6565185 | Institute of Molecular Genetics of the Czech Academy of Sciences | ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565185|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 EaD | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E MTAB 8800:WKM 7 EaD s | WKM 7 EaD s | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | Experimental Factor: stimulus:kit ligand | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | SINGLE | ILLUMINA | NextSeq 500 | ERP120057 | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | 11_WKM_7_EaD_1.fastq.gz | fastq | 3127207407.0 | 41417754.0 | E MTAB 8800:WKM 7 EaD | 0:75.50 1:0 | A:618290483;C:948661192;G:891134088;T:669046822;N:74822 | 75 | 0 | 618290483 | 948661192 | 891134088 | 669046822 | 74822 | ERX3938951 | ERS4329528 | ERA2383450 | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | 1 | 0.96441 | 0.20171 | 0.85427 | 0.75425 | 76 | B | usable mapping rate | illumina | nextseq | full_length | rrna_depletion | smarter | bulk | bulk | bulk | Czech Republic | 2021-12-31 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||
| 9814 | 9814 | ERR3931360 | ERX3938950 | ERS4329527 | ERP120057 | PRJEB36819 | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E-MTAB-8800 | Transcriptome Analysis | Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | WKM 5 ED | SAMEA6565184 | Institute of Molecular Genetics of the Czech Academy of Sciences | ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565184|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 ED | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E MTAB 8800:WKM 5 ED s | WKM 5 ED s | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | Experimental Factor: stimulus:n1 | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | SINGLE | ILLUMINA | NextSeq 500 | ERP120057 | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | 8_WKM_5_ED.fastq.gz | fastq | 3762435507.0 | 49825705.0 | E MTAB 8800:WKM 5 ED | 0:75.51 1:0 | A:760573477;C:1107794761;G:1060998015;T:832975681;N:93573 | 75 | 0 | 760573477 | 1107794761 | 1060998015 | 832975681 | 93573 | ERX3938950 | ERS4329527 | ERA2383450 | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | 1 | 0.96233 | 0.20628 | 0.84141 | 0.73601 | 75 | B | usable mapping rate | illumina | nextseq | full_length | rrna_depletion | smarter | bulk | bulk | bulk | Czech Republic | 2021-12-31 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||
| 9815 | 9815 | ERR3931359 | ERX3938949 | ERS4329526 | ERP120057 | PRJEB36819 | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E-MTAB-8800 | Transcriptome Analysis | Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | WKM 5 EaD | SAMEA6565183 | Institute of Molecular Genetics of the Czech Academy of Sciences | ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565183|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 EaD | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E MTAB 8800:WKM 5 EaD s | WKM 5 EaD s | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | Experimental Factor: stimulus:kit ligand | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | SINGLE | ILLUMINA | NextSeq 500 | ERP120057 | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | 9_WKM_5_EaD.fastq.gz | fastq | 3602342027.0 | 47707938.0 | E MTAB 8800:WKM 5 EaD | 0:75.51 1:0 | A:717278291;C:1084375347;G:1027250408;T:773351695;N:86286 | 75 | 0 | 717278291 | 1084375347 | 1027250408 | 773351695 | 86286 | ERX3938949 | ERS4329526 | ERA2383450 | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | 1 | 0.96461 | 0.20281 | 0.85303 | 0.74553 | 75 | B | usable mapping rate | illumina | nextseq | full_length | rrna_depletion | smarter | bulk | bulk | bulk | Czech Republic | 2021-12-31 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||
| 15028 | 15028 | ERR594449 | ERX552402 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 010 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_010_R1.fastq.gz McGrail_PT_MM02_010_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 010 R | 0:100 1:100 | A:871527648;C:730105705;G:727172263;T:866698092;N:4496292 | 100 | 100 | 871527648 | 730105705 | 727172263 | 866698092 | 4496292 | ERX552402 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92177 | 0.92501 | 0.1237 | 0.1262 | 0.69844 | 0.7009 | 0.49781 | 0.4982 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15029 | 15029 | ERR594457 | ERX552401 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 002 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_002_R1.fastq.gz McGrail_PT_MM02_002_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 002 R | 0:100 1:100 | A:872387737;C:732112926;G:726274702;T:868026782;N:1197853 | 100 | 100 | 872387737 | 732112926 | 726274702 | 868026782 | 1197853 | ERX552401 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92719 | 0.92684 | 0.126 | 0.12696 | 0.69684 | 0.70118 | 0.49645 | 0.50037 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15030 | 15030 | ERR594456 | ERX552400 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 004 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_004_R2.fastq.gz McGrail_T_MM01_004_R1.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 004 R | 0:100 1:100 | A:849885320;C:752565271;G:741295555;T:853272249;N:2981605 | 100 | 100 | 849885320 | 752565271 | 741295555 | 853272249 | 2981605 | ERX552400 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93431 | 0.93209 | 0.09121 | 0.09114 | 0.67842 | 0.68065 | 0.49543 | 0.48591 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15031 | 15031 | ERR594431 | ERX552399 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 014 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_014_R1.fastq.gz MM03_WT_L003_014_R2.fastq.gz | fastq fastq | 2051137800.0 | 10255689.0 | E MTAB 2886:MM03 WT L003 014 R | 0:100 1:100 | A:574425675;C:454197762;G:448836898;T:573386204;N:291261 | 100 | 100 | 574425675 | 454197762 | 448836898 | 573386204 | 291261 | ERX552399 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91659 | 0.91612 | 0.14679 | 0.14915 | 0.7163 | 0.72188 | 0.49275 | 0.49876 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15032 | 15032 | ERR594437 | ERX552398 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 006 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_006_R1.fastq.gz MM03_WT_L003_006_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 006 R | 0:100 1:100 | A:892528148;C:712696530;G:702466589;T:891189817;N:1118916 | 100 | 100 | 892528148 | 712696530 | 702466589 | 891189817 | 1118916 | ERX552398 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91798 | 0.9161 | 0.14538 | 0.14613 | 0.71401 | 0.71656 | 0.48443 | 0.48666 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15033 | 15033 | ERR594420 | ERX552397 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 014 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_014_R1.fastq.gz McGrail_PT_MM02_014_R2.fastq.gz | fastq fastq | 2883852800.0 | 14419264.0 | E MTAB 2886:McGrail PT MM02 014 R | 0:100 1:100 | A:787372572;C:658074713;G:654251401;T:783994205;N:159909 | 100 | 100 | 787372572 | 658074713 | 654251401 | 783994205 | 159909 | ERX552397 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92417 | 0.9255 | 0.12479 | 0.12619 | 0.69942 | 0.7035 | 0.50149 | 0.49379 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15034 | 15034 | ERR594450 | ERX552396 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 014 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_014_R1.fastq.gz McGrail_T_MM01_014_R2.fastq.gz | fastq fastq | 632445400.0 | 3162227.0 | E MTAB 2886:McGrail T MM01 014 R | 0:100 1:100 | A:168708082;C:147923885;G:146292680;T:169438791;N:81962 | 100 | 100 | 168708082 | 147923885 | 146292680 | 169438791 | 81962 | ERX552396 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93335 | 0.93318 | 0.09287 | 0.09485 | 0.68205 | 0.68846 | 0.4841 | 0.49015 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15035 | 15035 | ERR594453 | ERX552395 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 011 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_011_R1.fastq.gz McGrail_T_MM01_011_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 011 R | 0:100 1:100 | A:852133250;C:751414688;G:741468348;T:854136333;N:847381 | 100 | 100 | 852133250 | 751414688 | 741468348 | 854136333 | 847381 | ERX552395 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93354 | 0.93309 | 0.09259 | 0.09299 | 0.68085 | 0.68347 | 0.48686 | 0.48742 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15036 | 15036 | ERR594429 | ERX552394 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 002 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_002_R1.fastq.gz McGrail_T_MM01_002_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 002 R | 0:100 1:100 | A:851061858;C:752624348;G:741241133;T:854588994;N:483667 | 100 | 100 | 851061858 | 752624348 | 741241133 | 854588994 | 483667 | ERX552394 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.9341 | 0.93285 | 0.09214 | 0.09303 | 0.68036 | 0.68465 | 0.4888 | 0.4918 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15037 | 15037 | ERR594444 | ERX552393 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 007 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_007_R1.fastq.gz McGrail_PT_MM02_007_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 007 R | 0:100 1:100 | A:871235248;C:733455837;G:726280934;T:868628388;N:399593 | 100 | 100 | 871235248 | 733455837 | 726280934 | 868628388 | 399593 | ERX552393 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92587 | 0.9237 | 0.12434 | 0.12596 | 0.69729 | 0.70473 | 0.49751 | 0.49568 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15038 | 15038 | ERR594436 | ERX552392 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 010 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_010_R1.fastq.gz MM03_WT_L003_010_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 010 R | 0:100 1:100 | A:893317570;C:712391457;G:703064824;T:890653459;N:572690 | 100 | 100 | 893317570 | 712391457 | 703064824 | 890653459 | 572690 | ERX552392 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91775 | 0.91713 | 0.14296 | 0.14486 | 0.7136 | 0.71638 | 0.50074 | 0.49246 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15039 | 15039 | ERR594454 | ERX552391 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 003 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_003_R1.fastq.gz MM03_WT_L003_003_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 003 R | 0:100 1:100 | A:891513936;C:713529681;G:702140879;T:891351829;N:1463675 | 100 | 100 | 891513936 | 713529681 | 702140879 | 891351829 | 1463675 | ERX552391 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91714 | 0.91621 | 0.14364 | 0.14479 | 0.71384 | 0.71967 | 0.48172 | 0.4892 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15040 | 15040 | ERR594422 | ERX552378 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 001 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_001_R1.fastq.gz McGrail_T_MM01_001_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 001 R | 0:100 1:100 | A:849397709;C:754334352;G:741772141;T:853832972;N:662826 | 100 | 100 | 849397709 | 754334352 | 741772141 | 853832972 | 662826 | ERX552378 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93478 | 0.93297 | 0.09219 | 0.09261 | 0.67949 | 0.68205 | 0.48892 | 0.47759 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15041 | 15041 | ERR594433 | ERX552377 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 009 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_009_R1.fastq.gz MM03_WT_L003_009_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 009 R | 0:100 1:100 | A:895908752;C:709459693;G:701325342;T:892915017;N:391196 | 100 | 100 | 895908752 | 709459693 | 701325342 | 892915017 | 391196 | ERX552377 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91776 | 0.91744 | 0.14402 | 0.14626 | 0.71435 | 0.71794 | 0.48624 | 0.49768 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15042 | 15042 | ERR594419 | ERX552376 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 011 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_011_R1.fastq.gz MM03_WT_L003_011_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 011 R | 0:100 1:100 | A:894536120;C:711072714;G:702055612;T:891872676;N:462878 | 100 | 100 | 894536120 | 711072714 | 702055612 | 891872676 | 462878 | ERX552376 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91628 | 0.91598 | 0.14427 | 0.14587 | 0.71293 | 0.71575 | 0.48688 | 0.49317 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15043 | 15043 | ERR594447 | ERX552375 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 004 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_004_R1.fastq.gz MM03_WT_L003_004_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 004 R | 0:100 1:100 | A:893087129;C:711953975;G:702111417;T:891168240;N:1679239 | 100 | 100 | 893087129 | 711953975 | 702111417 | 891168240 | 1679239 | ERX552375 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91793 | 0.91708 | 0.14418 | 0.1457 | 0.71052 | 0.71405 | 0.50617 | 0.49339 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15044 | 15044 | ERR594441 | ERX552374 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 004 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_004_R1.fastq.gz McGrail_PT_MM02_004_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 004 R | 0:100 1:100 | A:869694755;C:734631291;G:727458512;T:866857422;N:1358020 | 100 | 100 | 869694755 | 734631291 | 727458512 | 866857422 | 1358020 | ERX552374 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92607 | 0.9248 | 0.12414 | 0.12446 | 0.69686 | 0.6995 | 0.50202 | 0.50333 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15045 | 15045 | ERR594455 | ERX552373 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 002 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_002_R1.fastq.gz MM03_WT_L003_002_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 002 R | 0:100 1:100 | A:894222634;C:711188537;G:702167816;T:891816353;N:604660 | 100 | 100 | 894222634 | 711188537 | 702167816 | 891816353 | 604660 | ERX552373 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.9174 | 0.91577 | 0.14516 | 0.14534 | 0.71342 | 0.71756 | 0.48084 | 0.50033 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15046 | 15046 | ERR594439 | ERX552410 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 007 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_007_R1.fastq.gz McGrail_T_MM01_007_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 007 R | 0:100 1:100 | A:850777874;C:752786693;G:741650641;T:854268527;N:516265 | 100 | 100 | 850777874 | 752786693 | 741650641 | 854268527 | 516265 | ERX552410 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93398 | 0.93264 | 0.0917 | 0.09232 | 0.67878 | 0.68172 | 0.48311 | 0.48417 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15047 | 15047 | ERR594426 | ERX552409 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 012 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_012_R1.fastq.gz McGrail_T_MM01_012_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 012 R | 0:100 1:100 | A:851190790;C:752415289;G:742719596;T:852979263;N:695062 | 100 | 100 | 851190790 | 752415289 | 742719596 | 852979263 | 695062 | ERX552409 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93297 | 0.9327 | 0.09093 | 0.09105 | 0.68043 | 0.68282 | 0.48563 | 0.48327 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15048 | 15048 | ERR594417 | ERX552390 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 007 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_007_R1.fastq.gz MM03_WT_L003_007_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 007 R | 0:100 1:100 | A:893566548;C:711756657;G:701577232;T:892509486;N:590077 | 100 | 100 | 893566548 | 711756657 | 701577232 | 892509486 | 590077 | ERX552390 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.9176 | 0.91644 | 0.14542 | 0.14641 | 0.71358 | 0.71713 | 0.48742 | 0.50207 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15049 | 15049 | ERR594418 | ERX552389 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 008 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_008_R1.fastq.gz McGrail_T_MM01_008_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 008 R | 0:100 1:100 | A:851314323;C:752411525;G:742349039;T:853577153;N:347960 | 100 | 100 | 851314323 | 752411525 | 742349039 | 853577153 | 347960 | ERX552389 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93343 | 0.93187 | 0.09175 | 0.09249 | 0.68016 | 0.68164 | 0.47952 | 0.48824 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15050 | 15050 | ERR594440 | ERX552388 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 013 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_013_R1.fastq.gz McGrail_T_MM01_013_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 013 R | 0:100 1:100 | A:852425880;C:750595968;G:742140159;T:854286637;N:551356 | 100 | 100 | 852425880 | 750595968 | 742140159 | 854286637 | 551356 | ERX552388 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93231 | 0.93338 | 0.09134 | 0.09313 | 0.67945 | 0.68256 | 0.48693 | 0.48084 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15051 | 15051 | ERR594430 | ERX552387 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 006 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_006_R1.fastq.gz McGrail_PT_MM02_006_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 006 R | 0:100 1:100 | A:869575312;C:734964855;G:727824124;T:866586174;N:1049535 | 100 | 100 | 869575312 | 734964855 | 727824124 | 866586174 | 1049535 | ERX552387 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.9265 | 0.92348 | 0.12368 | 0.12345 | 0.69818 | 0.70017 | 0.4966 | 0.50082 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15052 | 15052 | ERR594445 | ERX552386 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 012 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_012_R1.fastq.gz McGrail_PT_MM02_012_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 012 R | 0:100 1:100 | A:870939166;C:729921300;G:724359208;T:865762186;N:9018140 | 100 | 100 | 870939166 | 729921300 | 724359208 | 865762186 | 9018140 | ERX552386 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92143 | 0.92467 | 0.1229 | 0.12533 | 0.69828 | 0.70015 | 0.50049 | 0.4981 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15053 | 15053 | ERR594434 | ERX552385 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 013 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_013_R1.fastq.gz MM03_WT_L003_013_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 013 R | 0:100 1:100 | A:894614606;C:711109946;G:702301073;T:891485450;N:488925 | 100 | 100 | 894614606 | 711109946 | 702301073 | 891485450 | 488925 | ERX552385 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91697 | 0.91671 | 0.1447 | 0.14584 | 0.71327 | 0.7176 | 0.48116 | 0.49462 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15054 | 15054 | ERR594443 | ERX552372 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 011 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_011_R1.fastq.gz McGrail_PT_MM02_011_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 011 R | 0:100 1:100 | A:869080240;C:728959737;G:723451216;T:862492567;N:16016240 | 100 | 100 | 869080240 | 728959737 | 723451216 | 862492567 | 16016240 | ERX552372 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91732 | 0.92471 | 0.12164 | 0.12427 | 0.69739 | 0.69773 | 0.50246 | 0.50104 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15055 | 15055 | ERR594425 | ERX552371 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 003 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_003_R1.fastq.gz McGrail_T_MM01_003_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 003 R | 0:100 1:100 | A:849037687;C:754289116;G:741157518;T:854195808;N:1319871 | 100 | 100 | 849037687 | 754289116 | 741157518 | 854195808 | 1319871 | ERX552371 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93418 | 0.93244 | 0.09187 | 0.09177 | 0.67919 | 0.68278 | 0.49475 | 0.4843 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15056 | 15056 | ERR594442 | ERX552370 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 013 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_013_R1.fastq.gz McGrail_PT_MM02_013_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 013 R | 0:100 1:100 | A:871688870;C:733183478;G:727799783;T:867055926;N:271943 | 100 | 100 | 871688870 | 733183478 | 727799783 | 867055926 | 271943 | ERX552370 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92516 | 0.92506 | 0.12387 | 0.12596 | 0.69601 | 0.69852 | 0.49866 | 0.50071 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15057 | 15057 | ERR594438 | ERX552369 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 005 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_005_R1.fastq.gz McGrail_T_MM01_005_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 005 R | 0:100 1:100 | A:849484270;C:753864282;G:741293874;T:854126120;N:1231454 | 100 | 100 | 849484270 | 753864282 | 741293874 | 854126120 | 1231454 | ERX552369 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93385 | 0.93181 | 0.09285 | 0.0935 | 0.67882 | 0.68209 | 0.48445 | 0.49581 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15058 | 15058 | ERR594452 | ERX552408 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 001 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_001_R1.fastq.gz McGrail_PT_MM02_001_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 001 R | 0:100 1:100 | A:869685021;C:734763957;G:726895796;T:867397539;N:1257687 | 100 | 100 | 869685021 | 734763957 | 726895796 | 867397539 | 1257687 | ERX552408 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92687 | 0.92533 | 0.12345 | 0.12461 | 0.69749 | 0.70055 | 0.49809 | 0.49848 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15059 | 15059 | ERR594446 | ERX552407 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 006 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_006_R1.fastq.gz McGrail_T_MM01_006_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 006 R | 0:100 1:100 | A:850456499;C:753116092;G:742193025;T:853616872;N:617512 | 100 | 100 | 850456499 | 753116092 | 742193025 | 853616872 | 617512 | ERX552407 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.9331 | 0.93179 | 0.09172 | 0.09219 | 0.67917 | 0.68158 | 0.48168 | 0.48339 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15060 | 15060 | ERR594428 | ERX552406 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 008 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_008_R1.fastq.gz McGrail_PT_MM02_008_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 008 R | 0:100 1:100 | A:871557679;C:733260378;G:727404860;T:867366205;N:410878 | 100 | 100 | 871557679 | 733260378 | 727404860 | 867366205 | 410878 | ERX552406 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92806 | 0.92602 | 0.12481 | 0.12546 | 0.69771 | 0.70086 | 0.50152 | 0.50006 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15061 | 15061 | ERR594423 | ERX552405 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 008 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_008_R1.fastq.gz MM03_WT_L003_008_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 008 R | 0:100 1:100 | A:894053419;C:711591129;G:702881160;T:891029747;N:444545 | 100 | 100 | 894053419 | 711591129 | 702881160 | 891029747 | 444545 | ERX552405 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91542 | 0.91567 | 0.14469 | 0.14612 | 0.71289 | 0.7161 | 0.49104 | 0.48972 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15062 | 15062 | ERR594424 | ERX552404 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 005 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_005_R1.fastq.gz MM03_WT_L003_005_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 005 R | 0:100 1:100 | A:892331319;C:712533931;G:701570336;T:891914366;N:1650048 | 100 | 100 | 892331319 | 712533931 | 701570336 | 891914366 | 1650048 | ERX552404 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91746 | 0.91624 | 0.14471 | 0.14581 | 0.71498 | 0.71985 | 0.48939 | 0.49411 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15063 | 15063 | ERR594416 | ERX552403 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 005 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_005_R1.fastq.gz McGrail_PT_MM02_005_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 005 R | 0:100 1:100 | A:870557258;C:733600250;G:726156781;T:868210376;N:1475335 | 100 | 100 | 870557258 | 733600250 | 726156781 | 868210376 | 1475335 | ERX552403 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92621 | 0.92323 | 0.12426 | 0.1247 | 0.69836 | 0.70418 | 0.50259 | 0.49996 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15064 | 15064 | ERR594427 | ERX552384 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 009 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_009_R1.fastq.gz McGrail_PT_MM02_009_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 009 R | 0:100 1:100 | A:872849771;C:731277001;G:727186355;T:868245858;N:441015 | 100 | 100 | 872849771 | 731277001 | 727186355 | 868245858 | 441015 | ERX552384 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92396 | 0.92581 | 0.12417 | 0.12625 | 0.69879 | 0.70189 | 0.50046 | 0.50188 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15065 | 15065 | ERR594432 | ERX552383 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 010 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_010_R1.fastq.gz McGrail_T_MM01_010_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 010 R | 0:100 1:100 | A:850551531;C:753023540;G:742554950;T:852763762;N:1106217 | 100 | 100 | 850551531 | 753023540 | 742554950 | 852763762 | 1106217 | ERX552383 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93373 | 0.93132 | 0.09087 | 0.09072 | 0.67898 | 0.68083 | 0.49414 | 0.48713 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15066 | 15066 | ERR594435 | ERX552382 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 009 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_009_R1.fastq.gz McGrail_T_MM01_009_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 009 R | 0:100 1:100 | A:852308329;C:751198229;G:741341036;T:854788512;N:363894 | 100 | 100 | 852308329 | 751198229 | 741341036 | 854788512 | 363894 | ERX552382 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93348 | 0.93139 | 0.09329 | 0.09409 | 0.68071 | 0.68359 | 0.48469 | 0.49176 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15067 | 15067 | ERR594421 | ERX552381 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 012 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_012_R1.fastq.gz MM03_WT_L003_012_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 012 R | 0:100 1:100 | A:894330816;C:710946707;G:702107786;T:892049601;N:565090 | 100 | 100 | 894330816 | 710946707 | 702107786 | 892049601 | 565090 | ERX552381 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91723 | 0.91629 | 0.14541 | 0.14611 | 0.71427 | 0.71719 | 0.49682 | 0.49865 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15068 | 15068 | ERR594451 | ERX552380 | ERS539976 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM03 WT | SAMEA2747168 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:MM03 WT L003 001 | MM03 WT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | MM03_WT_L003_001_R1.fastq.gz MM03_WT_L003_001_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:MM03 WT L003 001 R | 0:100 1:100 | A:892492791;C:713070365;G:702444959;T:891434993;N:556892 | 100 | 100 | 892492791 | 713070365 | 702444959 | 891434993 | 556892 | ERX552380 | ERS539976 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.91795 | 0.91727 | 0.14627 | 0.14672 | 0.71382 | 0.71636 | 0.48819 | 0.49971 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 15069 | 15069 | ERR594448 | ERX552379 | ERS539975 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM02 PT | SAMEA2747167 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail PT MM02 003 | MM02 PT | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_PT_MM02_003_R1.fastq.gz McGrail_PT_MM02_003_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail PT MM02 003 R | 0:100 1:100 | A:870188856;C:734020429;G:726554216;T:867996712;N:1239787 | 100 | 100 | 870188856 | 734020429 | 726554216 | 867996712 | 1239787 | ERX552379 | ERS539975 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.92516 | 0.92471 | 0.12313 | 0.12411 | 0.69686 | 0.69982 | 0.49257 | 0.49644 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 25345 | 25345 | SRR25868018 | SRX21589435 | SRS18767008 | SRP457978 | PRJNA1011839 | fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk] | GSE242134 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | 20m des trunk group 3 | GSM7749541 | source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing | 20m des trunk group 3 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | 20 mpf trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / | GSM7749541 | GSM7749541: 20m des trunk group 3; Danio rerio; RNA Seq | GSM7749541 r1 | GSM7749541 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457978 | loader:fastq load.py | P25101_112_S23_L003_R1_001.fastq.gz P25101_112_S23_L003_R2_001.fastq.gz | fastq fastq | 22210763348.0 | 73545574.0 | GSM7749541 r1 | 0:151 1:151 | A:5912051069;C:5198859790;G:5393563455;T:5706179211;N:109823 | 151 | 151 | 5912051069 | 5198859790 | 5393563455 | 5706179211 | 109823 | SRX21589435 | SRS18767008 | SRA1703875 | Umeå Univeristy | Umeå Univeristy | 2 | 0.95876 | 0.95266 | 0.03675 | 0.03686 | 0.80085 | 0.80379 | 0.54105 | 0.54121 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25346 | 25346 | SRR25868019 | SRX21589434 | SRS18767007 | SRP457978 | PRJNA1011839 | fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk] | GSE242134 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | 20m des trunk group 2 | GSM7749540 | source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing | 20m des trunk group 2 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | 20 mpf trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / | GSM7749540 | GSM7749540: 20m des trunk group 2; Danio rerio; RNA Seq | GSM7749540 r1 | GSM7749540 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457978 | loader:fastq load.py | P25101_111_S22_L003_R1_001.fastq.gz P25101_111_S22_L003_R2_001.fastq.gz | fastq fastq | 28432907098.0 | 94148699.0 | GSM7749540 r1 | 0:151 1:151 | A:7530352460;C:6691515017;G:7032193813;T:7178705133;N:140675 | 151 | 151 | 7530352460 | 6691515017 | 7032193813 | 7178705133 | 140675 | SRX21589434 | SRS18767007 | SRA1703875 | Umeå Univeristy | Umeå Univeristy | 2 | 0.95304 | 0.94619 | 0.0303 | 0.03073 | 0.81288 | 0.81734 | 0.54159 | 0.529 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25347 | 25347 | SRR25868020 | SRX21589433 | SRS18767006 | SRP457978 | PRJNA1011839 | fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk] | GSE242134 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | 20m des trunk group 1 | GSM7749539 | source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing | 20m des trunk group 1 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | 20 mpf trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / | GSM7749539 | GSM7749539: 20m des trunk group 1; Danio rerio; RNA Seq | GSM7749539 r1 | GSM7749539 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457978 | loader:fastq load.py | P25101_110_S21_L003_R1_001.fastq.gz P25101_110_S21_L003_R2_001.fastq.gz | fastq fastq | 22459067748.0 | 74367774.0 | GSM7749539 r1 | 0:151 1:151 | A:6073562522;C:5194312729;G:5517056007;T:5674024886;N:111604 | 151 | 151 | 6073562522 | 5194312729 | 5517056007 | 5674024886 | 111604 | SRX21589433 | SRS18767006 | SRA1703875 | Umeå Univeristy | Umeå Univeristy | 2 | 0.95491 | 0.94862 | 0.03326 | 0.03384 | 0.8047 | 0.80949 | 0.54962 | 0.53948 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25348 | 25348 | SRR25868021 | SRX21589432 | SRS18767005 | SRP457978 | PRJNA1011839 | fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk] | GSE242134 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | 20m wt trunk group 3 | GSM7749538 | source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing | 20m wt trunk group 3 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | 20 mpf trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT | GSM7749538 | GSM7749538: 20m wt trunk group 3; Danio rerio; RNA Seq | GSM7749538 r1 | GSM7749538 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457978 | loader:fastq load.py | P25101_109_S20_L003_R1_001.fastq.gz P25101_109_S20_L003_R2_001.fastq.gz | fastq fastq | 18161226926.0 | 60136513.0 | GSM7749538 r1 | 0:151 1:151 | A:4953172808;C:4151930418;G:4504584090;T:4551451588;N:88022 | 151 | 151 | 4953172808 | 4151930418 | 4504584090 | 4551451588 | 88022 | SRX21589432 | SRS18767005 | SRA1703875 | Umeå Univeristy | Umeå Univeristy | 2 | 0.94707 | 0.93454 | 0.03335 | 0.03308 | 0.80127 | 0.80708 | 0.56515 | 0.57038 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25349 | 25349 | SRR25868022 | SRX21589431 | SRS18767004 | SRP457978 | PRJNA1011839 | fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk] | GSE242134 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | 20m wt trunk group 2 | GSM7749537 | source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing | 20m wt trunk group 2 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | 20 mpf trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT | GSM7749537 | GSM7749537: 20m wt trunk group 2; Danio rerio; RNA Seq | GSM7749537 r1 | GSM7749537 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457978 | loader:fastq load.py | P25101_108_S19_L003_R1_001.fastq.gz P25101_108_S19_L003_R2_001.fastq.gz | fastq fastq | 21168501250.0 | 70094375.0 | GSM7749537 r1 | 0:151 1:151 | A:5676216227;C:4922704340;G:5191762300;T:5377713558;N:104825 | 151 | 151 | 5676216227 | 4922704340 | 5191762300 | 5377713558 | 104825 | SRX21589431 | SRS18767004 | SRA1703875 | Umeå Univeristy | Umeå Univeristy | 2 | 0.95544 | 0.94706 | 0.03451 | 0.03439 | 0.80998 | 0.81339 | 0.53843 | 0.50395 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25350 | 25350 | SRR25868023 | SRX21589430 | SRS18767003 | SRP457978 | PRJNA1011839 | fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk] | GSE242134 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | 20m wt trunk group 1 | GSM7749536 | source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing | 20m wt trunk group 1 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | 20 mpf trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT | GSM7749536 | GSM7749536: 20m wt trunk group 1; Danio rerio; RNA Seq | GSM7749536 r1 | GSM7749536 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457978 | loader:fastq load.py | P25101_107_S18_L003_R1_001.fastq.gz P25101_107_S18_L003_R2_001.fastq.gz | fastq fastq | 21809914520.0 | 72218260.0 | GSM7749536 r1 | 0:151 1:151 | A:5826455436;C:5083672325;G:5302648618;T:5597031501;N:106640 | 151 | 151 | 5826455436 | 5083672325 | 5302648618 | 5597031501 | 106640 | SRX21589430 | SRS18767003 | SRA1703875 | Umeå Univeristy | Umeå Univeristy | 2 | 0.96041 | 0.95117 | 0.03443 | 0.03455 | 0.80598 | 0.80872 | 0.50583 | 0.4806 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25357 | 25357 | SRR25868059 | SRX21589476 | SRS18767049 | SRP457980 | PRJNA1011841 | fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk] | GSE242136 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | des trunk group 3 | GSM7749569 | source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing | des trunk group 3 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / | GSM7749569 | GSM7749569: des trunk group 3; Danio rerio; RNA Seq | GSM7749569 r1 | GSM7749569 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457980 | loader:fastq load.py | P17251_112_S16_L001_R1_001.fastq.gz P17251_112_S16_L001_R2_001.fastq.gz | fastq fastq | 32975158332.0 | 109189266.0 | GSM7749569 r1 | 0:151 1:151 | A:8971397485;C:7542039111;G:8200961544;T:8260356002;N:404190 | 151 | 151 | 8971397485 | 7542039111 | 8200961544 | 8260356002 | 404190 | SRX21589476 | SRS18767049 | SRA1703878 | Umeå Univeristy | Umeå Univeristy | 2 | 0.9452 | 0.93318 | 0.03379 | 0.0337 | 0.80586 | 0.81485 | 0.56577 | 0.57552 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25358 | 25358 | SRR25868060 | SRX21589475 | SRS18767048 | SRP457980 | PRJNA1011841 | fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk] | GSE242136 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | des trunk group 2 | GSM7749568 | source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing | des trunk group 2 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / | GSM7749568 | GSM7749568: des trunk group 2; Danio rerio; RNA Seq | GSM7749568 r1 | GSM7749568 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457980 | loader:fastq load.py | P17251_111_S15_L001_R1_001.fastq.gz P17251_111_S15_L001_R2_001.fastq.gz | fastq fastq | 30771044854.0 | 101890877.0 | GSM7749568 r1 | 0:151 1:151 | A:8428723125;C:6962884900;G:7664589629;T:7714459134;N:388066 | 151 | 151 | 8428723125 | 6962884900 | 7664589629 | 7714459134 | 388066 | SRX21589475 | SRS18767048 | SRA1703878 | Umeå Univeristy | Umeå Univeristy | 2 | 0.94539 | 0.80414 | 0.03024 | 0.02542 | 0.8464 | 0.86281 | 0.50835 | 0.55329 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25359 | 25359 | SRR25868061 | SRX21589474 | SRS18767045 | SRP457980 | PRJNA1011841 | fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk] | GSE242136 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | des trunk group 1 | GSM7749567 | source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing | des trunk group 1 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / | GSM7749567 | GSM7749567: des trunk group 1; Danio rerio; RNA Seq | GSM7749567 r1 | GSM7749567 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457980 | loader:fastq load.py | P17251_110_S14_L001_R1_001.fastq.gz P17251_110_S14_L001_R2_001.fastq.gz | fastq fastq | 33874542116.0 | 112167358.0 | GSM7749567 r1 | 0:151 1:151 | A:8845255279;C:8046911900;G:8618139910;T:8363818933;N:416094 | 151 | 151 | 8845255279 | 8046911900 | 8618139910 | 8363818933 | 416094 | SRX21589474 | SRS18767045 | SRA1703878 | Umeå Univeristy | Umeå Univeristy | 2 | 0.94628 | 0.9369 | 0.02168 | 0.02198 | 0.83252 | 0.83816 | 0.5082 | 0.51978 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25360 | 25360 | SRR25868062 | SRX21589473 | SRS18767047 | SRP457980 | PRJNA1011841 | fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk] | GSE242136 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | wt trunk group 3 | GSM7749566 | source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing | wt trunk group 3 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT | GSM7749566 | GSM7749566: wt trunk group 3; Danio rerio; RNA Seq | GSM7749566 r1 | GSM7749566 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457980 | loader:fastq load.py | P17251_109_S13_L001_R1_001.fastq.gz P17251_109_S13_L001_R2_001.fastq.gz | fastq fastq | 34282805044.0 | 113519222.0 | GSM7749566 r1 | 0:151 1:151 | A:9124351621;C:8034310406;G:8391950458;T:8731771604;N:420955 | 151 | 151 | 9124351621 | 8034310406 | 8391950458 | 8731771604 | 420955 | SRX21589473 | SRS18767047 | SRA1703878 | Umeå Univeristy | Umeå Univeristy | 2 | 0.95625 | 0.95068 | 0.03255 | 0.03282 | 0.80555 | 0.81081 | 0.5875 | 0.58319 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25361 | 25361 | SRR25868063 | SRX21589472 | SRS18767046 | SRP457980 | PRJNA1011841 | fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk] | GSE242136 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | wt trunk group 2 | GSM7749565 | source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing | wt trunk group 2 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT | GSM7749565 | GSM7749565: wt trunk group 2; Danio rerio; RNA Seq | GSM7749565 r1 | GSM7749565 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457980 | loader:fastq load.py | P17251_108_S12_L001_R1_001.fastq.gz P17251_108_S12_L001_R2_001.fastq.gz | fastq fastq | 29439584536.0 | 97482068.0 | GSM7749565 r1 | 0:151 1:151 | A:7923205722;C:6779291710;G:7327163186;T:7409562179;N:361739 | 151 | 151 | 7923205722 | 6779291710 | 7327163186 | 7409562179 | 361739 | SRX21589472 | SRS18767046 | SRA1703878 | Umeå Univeristy | Umeå Univeristy | 2 | 0.94148 | 0.933 | 0.03555 | 0.03563 | 0.80562 | 0.81302 | 0.53017 | 0.5746 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 25362 | 25362 | SRR25868064 | SRX21589471 | SRS18767044 | SRP457980 | PRJNA1011841 | fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk] | GSE242136 | Transcriptome Analysis | In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points. | parent bioproject:PRJNA1011837 | pubmed:38431640 | wt trunk group 1 | GSM7749564 | source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing | wt trunk group 1 | Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts | trunk muscle | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C | tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT | GSM7749564 | GSM7749564: wt trunk group 1; Danio rerio; RNA Seq | GSM7749564 r1 | GSM7749564 | 1 | Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP457980 | loader:fastq load.py | P17251_107_S11_L001_R1_001.fastq.gz P17251_107_S11_L001_R2_001.fastq.gz | fastq fastq | 30984282826.0 | 102596963.0 | GSM7749564 r1 | 0:151 1:151 | A:8167387484;C:7329431316;G:7662021788;T:7825061355;N:380883 | 151 | 151 | 8167387484 | 7329431316 | 7662021788 | 7825061355 | 380883 | SRX21589471 | SRS18767044 | SRA1703878 | Umeå Univeristy | Umeå Univeristy | 2 | 0.94444 | 0.93765 | 0.03334 | 0.03351 | 0.80089 | 0.80535 | 0.56476 | 0.50751 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | Sweden | 2023-09-01 | Adult | Adult | Multi-tissue | Multi-system | |||||||||
| 26518 | 26518 | SRR26050763 | SRX21767119 | SRS18873424 | SRP460207 | PRJNA1016321 | The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis | GSE243072 | Transcriptome Analysis | Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis. | pubmed:39171526 | psmb1 mutants 72hpf biological replicate 4 cranial sox10+ cells | GSM7778660 | source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing | psmb1 mutants 72hpf biological replicate 4 cranial sox10+ cells | Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples | cranial sox10+ cells neural crest/chondrocytes | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | Embryos were raised in E3 at 28.5C until 72hpf. | tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / | GSM7778660 | GSM7778660: psmb1 mutants 72hpf biological replicate 4 cranial sox10+ cells; Danio rerio; RNA Seq | GSM7778660 r1 | GSM7778660 | 1 | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP460207 | loader:fastq load.py | sox10_M4_R1_001.fastq.gz sox10_M4_R2_001.fastq.gz | fastq fastq | 17203316400.0 | 57344388.0 | GSM7778660 r1 | 0:150 1:150 | A:4557769784;C:4038080087;G:4028545423;T:4578857383;N:63723 | 150 | 150 | 4557769784 | 4038080087 | 4028545423 | 4578857383 | 63723 | SRX21767119 | SRS18873424 | SRA1711572 | BWH | BWH | 2 | 0.93924 | 0.93866 | 0.10703 | 0.1068 | 0.70597 | 0.70508 | 0.52195 | 0.52023 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cdna_unspecified | nextera | bulk | bulk | bulk | United States | 2023-09-13 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||
| 26519 | 26519 | SRR26050764 | SRX21767118 | SRS18873423 | SRP460207 | PRJNA1016321 | The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis | GSE243072 | Transcriptome Analysis | Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis. | pubmed:39171526 | psmb1 mutants 72hpf biological replicate 3 cranial sox10+ cells | GSM7778659 | source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing | psmb1 mutants 72hpf biological replicate 3 cranial sox10+ cells | Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples | cranial sox10+ cells neural crest/chondrocytes | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | Embryos were raised in E3 at 28.5C until 72hpf. | tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / | GSM7778659 | GSM7778659: psmb1 mutants 72hpf biological replicate 3 cranial sox10+ cells; Danio rerio; RNA Seq | GSM7778659 r1 | GSM7778659 | 1 | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP460207 | loader:fastq load.py | sox10_M3_R1_001.fastq.gz sox10_M3_R2_001.fastq.gz | fastq fastq | 16490564400.0 | 54968548.0 | GSM7778659 r1 | 0:150 1:150 | A:4465032867;C:3767540674;G:3755500192;T:4502428180;N:62487 | 150 | 150 | 4465032867 | 3767540674 | 3755500192 | 4502428180 | 62487 | SRX21767118 | SRS18873423 | SRA1711572 | BWH | BWH | 2 | 0.92805 | 0.92792 | 0.14244 | 0.14225 | 0.69639 | 0.69757 | 0.52133 | 0.52056 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cdna_unspecified | nextera | bulk | bulk | bulk | United States | 2023-09-13 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||
| 26520 | 26520 | SRR26050765 | SRX21767117 | SRS18873422 | SRP460207 | PRJNA1016321 | The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis | GSE243072 | Transcriptome Analysis | Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis. | pubmed:39171526 | psmb1 mutants 72hpf biological replicate 1 cranial sox10+ cells | GSM7778658 | source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing | psmb1 mutants 72hpf biological replicate 1 cranial sox10+ cells | Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples | cranial sox10+ cells neural crest/chondrocytes | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | Embryos were raised in E3 at 28.5C until 72hpf. | tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / | GSM7778658 | GSM7778658: psmb1 mutants 72hpf biological replicate 1 cranial sox10+ cells; Danio rerio; RNA Seq | GSM7778658 r1 | GSM7778658 | 1 | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP460207 | loader:fastq load.py | sox10_M1_R1_001.fastq.gz sox10_M1_R2_001.fastq.gz | fastq fastq | 14363136600.0 | 47877122.0 | GSM7778658 r1 | 0:150 1:150 | A:3843987690;C:3329370255;G:3310959116;T:3878765025;N:54514 | 150 | 150 | 3843987690 | 3329370255 | 3310959116 | 3878765025 | 54514 | SRX21767117 | SRS18873422 | SRA1711572 | BWH | BWH | 2 | 0.92722 | 0.92625 | 0.11695 | 0.11644 | 0.69611 | 0.6969 | 0.52036 | 0.522 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cdna_unspecified | nextera | bulk | bulk | bulk | United States | 2023-09-13 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||
| 26521 | 26521 | SRR26050766 | SRX21767116 | SRS18873421 | SRP460207 | PRJNA1016321 | The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis | GSE243072 | Transcriptome Analysis | Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis. | pubmed:39171526 | psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial sox10+ cells | GSM7778657 | source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing | psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial sox10+ cells | Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples | cranial sox10+ cells neural crest/chondrocytes | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | Embryos were raised in E3 at 28.5C until 72hpf. | tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ | GSM7778657 | GSM7778657: psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial sox10+ cells; Danio rerio; RNA Seq | GSM7778657 r1 | GSM7778657 | 1 | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP460207 | loader:fastq load.py | sox10_WH4_R1_001.fastq.gz sox10_WH4_R2_001.fastq.gz | fastq fastq | 14383303200.0 | 47944344.0 | GSM7778657 r1 | 0:150 1:150 | A:3825787510;C:3356860561;G:3322388892;T:3878211922;N:54315 | 150 | 150 | 3825787510 | 3356860561 | 3322388892 | 3878211922 | 54315 | SRX21767116 | SRS18873421 | SRA1711572 | BWH | BWH | 2 | 0.93157 | 0.93024 | 0.09771 | 0.09735 | 0.7177 | 0.71829 | 0.52664 | 0.52877 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cdna_unspecified | nextera | bulk | bulk | bulk | United States | 2023-09-13 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||
| 26522 | 26522 | SRR26050767 | SRX21767115 | SRS18873420 | SRP460207 | PRJNA1016321 | The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis | GSE243072 | Transcriptome Analysis | Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis. | pubmed:39171526 | psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial sox10+ cells | GSM7778656 | source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing | psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial sox10+ cells | Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples | cranial sox10+ cells neural crest/chondrocytes | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | Embryos were raised in E3 at 28.5C until 72hpf. | tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ | GSM7778656 | GSM7778656: psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial sox10+ cells; Danio rerio; RNA Seq | GSM7778656 r1 | GSM7778656 | 1 | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP460207 | loader:fastq load.py | sox10_WH3_R1_001.fastq.gz sox10_WH3_R2_001.fastq.gz | fastq fastq | 13772364600.0 | 45907882.0 | GSM7778656 r1 | 0:150 1:150 | A:3599468762;C:3277366623;G:3241941715;T:3653534992;N:52508 | 150 | 150 | 3599468762 | 3277366623 | 3241941715 | 3653534992 | 52508 | SRX21767115 | SRS18873420 | SRA1711572 | BWH | BWH | 2 | 0.94023 | 0.93961 | 0.07684 | 0.07628 | 0.70654 | 0.70682 | 0.50963 | 0.51111 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cdna_unspecified | nextera | bulk | bulk | bulk | United States | 2023-09-13 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||
| 26523 | 26523 | SRR26050768 | SRX21767114 | SRS18873419 | SRP460207 | PRJNA1016321 | The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis | GSE243072 | Transcriptome Analysis | Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis. | pubmed:39171526 | psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial sox10+ cells | GSM7778655 | source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing | psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial sox10+ cells | Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples | cranial sox10+ cells neural crest/chondrocytes | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | Embryos were raised in E3 at 28.5C until 72hpf. | tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ | GSM7778655 | GSM7778655: psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial sox10+ cells; Danio rerio; RNA Seq | GSM7778655 r1 | GSM7778655 | 1 | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP460207 | loader:fastq load.py | sox10_WH2_R1_001.fastq.gz sox10_WH2_R2_001.fastq.gz | fastq fastq | 15229813200.0 | 50766044.0 | GSM7778655 r1 | 0:150 1:150 | A:4029459993;C:3570808650;G:3534029380;T:4095461104;N:54073 | 150 | 150 | 4029459993 | 3570808650 | 3534029380 | 4095461104 | 54073 | SRX21767114 | SRS18873419 | SRA1711572 | BWH | BWH | 2 | 0.93346 | 0.93269 | 0.13006 | 0.13022 | 0.70094 | 0.70007 | 0.51067 | 0.50945 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cdna_unspecified | nextera | bulk | bulk | bulk | United States | 2023-09-13 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||
| 26524 | 26524 | SRR26050769 | SRX21767113 | SRS18873418 | SRP460207 | PRJNA1016321 | The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis | GSE243072 | Transcriptome Analysis | Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis. | pubmed:39171526 | psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial sox10+ cells | GSM7778654 | source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing | psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial sox10+ cells | Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples | cranial sox10+ cells neural crest/chondrocytes | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | Embryos were raised in E3 at 28.5C until 72hpf. | tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ | GSM7778654 | GSM7778654: psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial sox10+ cells; Danio rerio; RNA Seq | GSM7778654 r1 | GSM7778654 | 1 | 20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP460207 | loader:fastq load.py | sox10_WH1_R1_001.fastq.gz sox10_WH1_R2_001.fastq.gz | fastq fastq | 13483692600.0 | 44945642.0 | GSM7778654 r1 | 0:150 1:150 | A:3567731759;C:3163438678;G:3137216449;T:3615254758;N:50956 | 150 | 150 | 3567731759 | 3163438678 | 3137216449 | 3615254758 | 50956 | SRX21767113 | SRS18873418 | SRA1711572 | BWH | BWH | 2 | 0.92459 | 0.92408 | 0.11911 | 0.11956 | 0.7027 | 0.70264 | 0.50884 | 0.50322 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cdna_unspecified | nextera | bulk | bulk | bulk | United States | 2023-09-13 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||
| 35871 | 35871 | SRR33167498 | SRX28428354 | SRS24751227 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 2B L6.D708 | GSM8919410 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing | MB125 2B L6.D708 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1 | GSM8919410 | GSM8919410: MB125 2B L6.D708; Danio rerio; RNA Seq | GSM8919410 r1 | GSM8919410 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_2B_L6.D708_1.fastq.gz MB125_2B_L6.D708_2.fastq.gz | fastq fastq | 2319886164.0 | 22743982.0 | GSM8919410 r1 | 0:51 1:51 | A:553297266;C:587452449;G:584241025;T:594875512;N:19912 | 51 | 51 | 553297266 | 587452449 | 584241025 | 594875512 | 19912 | SRX28428354 | SRS24751227 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Multi-stage | Multi-stage | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35872 | 35872 | SRR33167499 | SRX28428353 | SRS24751225 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 1H L6.D705 | GSM8919409 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | MB125 1H L6.D705 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919409 | GSM8919409: MB125 1H L6.D705; Danio rerio; RNA Seq | GSM8919409 r1 | GSM8919409 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_1H_L6.D705_1.fastq.gz MB125_1H_L6.D705_2.fastq.gz | fastq fastq | 2373981966.0 | 23274333.0 | GSM8919409 r1 | 0:51 1:51 | A:568938101;C:599603085;G:595620007;T:609800208;N:20565 | 51 | 51 | 568938101 | 599603085 | 595620007 | 609800208 | 20565 | SRX28428353 | SRS24751225 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35873 | 35873 | SRR33167500 | SRX28428352 | SRS24751226 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 1G L6.D707 | GSM8919408 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | MB125 1G L6.D707 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919408 | GSM8919408: MB125 1G L6.D707; Danio rerio; RNA Seq | GSM8919408 r1 | GSM8919408 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_1G_L6.D707_1.fastq.gz MB125_1G_L6.D707_2.fastq.gz | fastq fastq | 2557560036.0 | 25074118.0 | GSM8919408 r1 | 0:51 1:51 | A:619676841;C:640365331;G:637208159;T:660287312;N:22393 | 51 | 51 | 619676841 | 640365331 | 637208159 | 660287312 | 22393 | SRX28428352 | SRS24751226 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35874 | 35874 | SRR33167501 | SRX28428351 | SRS24751224 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 1F L6.D706 | GSM8919407 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | MB125 1F L6.D706 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919407 | GSM8919407: MB125 1F L6.D706; Danio rerio; RNA Seq | GSM8919407 r1 | GSM8919407 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_1F_L6.D706_1.fastq.gz MB125_1F_L6.D706_2.fastq.gz | fastq fastq | 2646607362.0 | 25947131.0 | GSM8919407 r1 | 0:51 1:51 | A:620307465;C:682923030;G:678065242;T:665289569;N:22056 | 51 | 51 | 620307465 | 682923030 | 678065242 | 665289569 | 22056 | SRX28428351 | SRS24751224 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35875 | 35875 | SRR33167502 | SRX28428350 | SRS24751223 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 1D L6.D703 | GSM8919406 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | MB125 1D L6.D703 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919406 | GSM8919406: MB125 1D L6.D703; Danio rerio; RNA Seq | GSM8919406 r1 | GSM8919406 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_1D_L6.D703_1.fastq.gz MB125_1D_L6.D703_2.fastq.gz | fastq fastq | 2431917150.0 | 23842325.0 | GSM8919406 r1 | 0:51 1:51 | A:589729741;C:608847610;G:603837645;T:629482079;N:20075 | 51 | 51 | 589729741 | 608847610 | 603837645 | 629482079 | 20075 | SRX28428350 | SRS24751223 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35876 | 35876 | SRR33167503 | SRX28428349 | SRS24751222 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 1C L6.D704 | GSM8919405 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | MB125 1C L6.D704 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919405 | GSM8919405: MB125 1C L6.D704; Danio rerio; RNA Seq | GSM8919405 r1 | GSM8919405 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_1C_L6.D704_1.fastq.gz MB125_1C_L6.D704_2.fastq.gz | fastq fastq | 2525909130.0 | 24763815.0 | GSM8919405 r1 | 0:51 1:51 | A:624391801;C:621947668;G:618750869;T:660797379;N:21413 | 51 | 51 | 624391801 | 621947668 | 618750869 | 660797379 | 21413 | SRX28428349 | SRS24751222 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35877 | 35877 | SRR33167504 | SRX28428348 | SRS24751221 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 1A L6.D702 | GSM8919404 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | MB125 1A L6.D702 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919404 | GSM8919404: MB125 1A L6.D702; Danio rerio; RNA Seq | GSM8919404 r1 | GSM8919404 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_1A_L6.D702_1.fastq.gz MB125_1A_L6.D702_2.fastq.gz | fastq fastq | 2374806432.0 | 23282416.0 | GSM8919404 r1 | 0:51 1:51 | A:570636423;C:598720207;G:596247498;T:609181713;N:20591 | 51 | 51 | 570636423 | 598720207 | 596247498 | 609181713 | 20591 | SRX28428348 | SRS24751221 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35878 | 35878 | SRR33167505 | SRX28428347 | SRS24751220 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 CC7 S1 | GSM8919403 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing | GRC355 CC7 S1 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2 | GSM8919403 | GSM8919403: GRC355 CC7 S1; Danio rerio; RNA Seq | GSM8919403 r1 | GSM8919403 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_CC7_S1_R1_001.fastq.gz | fastq | 1602530400.0 | 21367072.0 | GSM8919403 r1 | 0:75 | A:423908384;C:380610264;G:430749077;T:367248932;N:13743 | 75 | 423908384 | 380610264 | 430749077 | 367248932 | 13743 | SRX28428347 | SRS24751220 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35879 | 35879 | SRR33167506 | SRX28428346 | SRS24751219 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 CC6 S13 | GSM8919402 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing | GRC355 CC6 S13 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2 | GSM8919402 | GSM8919402: GRC355 CC6 S13; Danio rerio; RNA Seq | GSM8919402 r1 | GSM8919402 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_CC6_S13_R1_001.fastq.gz | fastq | 2682385275.0 | 35765137.0 | GSM8919402 r1 | 0:75 | A:714420635;C:641843546;G:710142891;T:615939845;N:38358 | 75 | 714420635 | 641843546 | 710142891 | 615939845 | 38358 | SRX28428346 | SRS24751219 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35880 | 35880 | SRR33167507 | SRX28428345 | SRS24751218 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 CC5 S9 | GSM8919401 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing | GRC355 CC5 S9 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2 | GSM8919401 | GSM8919401: GRC355 CC5 S9; Danio rerio; RNA Seq | GSM8919401 r1 | GSM8919401 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_CC5_S9_R1_001.fastq.gz | fastq | 1963794750.0 | 26183930.0 | GSM8919401 r1 | 0:75 | A:526554394;C:453867368;G:498987697;T:484357818;N:27473 | 75 | 526554394 | 453867368 | 498987697 | 484357818 | 27473 | SRX28428345 | SRS24751218 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35881 | 35881 | SRR33167508 | SRX28428344 | SRS24751217 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 CC4 S6 | GSM8919400 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing | GRC355 CC4 S6 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2 | GSM8919400 | GSM8919400: GRC355 CC4 S6; Danio rerio; RNA Seq | GSM8919400 r1 | GSM8919400 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_CC4_S6_R1_001.fastq.gz | fastq | 2337900150.0 | 31172002.0 | GSM8919400 r1 | 0:75 | A:616059883;C:562202412;G:623837969;T:535779947;N:19939 | 75 | 616059883 | 562202412 | 623837969 | 535779947 | 19939 | SRX28428344 | SRS24751217 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35882 | 35882 | SRR33167509 | SRX28428343 | SRS24751216 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 CC3 S10 | GSM8919399 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing | GRC355 CC3 S10 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2 | GSM8919399 | GSM8919399: GRC355 CC3 S10; Danio rerio; RNA Seq | GSM8919399 r1 | GSM8919399 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_CC3_S10_R1_001.fastq.gz | fastq | 2438718375.0 | 32516245.0 | GSM8919399 r1 | 0:75 | A:649883373;C:579588054;G:640815663;T:568410218;N:21067 | 75 | 649883373 | 579588054 | 640815663 | 568410218 | 21067 | SRX28428343 | SRS24751216 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35883 | 35883 | SRR33167510 | SRX28428342 | SRS24751215 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 CC2 S12 | GSM8919398 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing | GRC355 CC2 S12 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2 | GSM8919398 | GSM8919398: GRC355 CC2 S12; Danio rerio; RNA Seq | GSM8919398 r1 | GSM8919398 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_CC2_S12_R1_001.fastq.gz | fastq | 2306185575.0 | 30749141.0 | GSM8919398 r1 | 0:75 | A:618466956;C:553097715;G:596880619;T:537720043;N:20242 | 75 | 618466956 | 553097715 | 596880619 | 537720043 | 20242 | SRX28428342 | SRS24751215 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35884 | 35884 | SRR33167511 | SRX28428341 | SRS24751214 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 CC1 S14 | GSM8919397 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing | GRC355 CC1 S14 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2 | GSM8919397 | GSM8919397: GRC355 CC1 S14; Danio rerio; RNA Seq | GSM8919397 r1 | GSM8919397 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_CC1_S14_R1_001.fastq.gz | fastq | 1666975950.0 | 22226346.0 | GSM8919397 r1 | 0:75 | A:444383649;C:378084847;G:409250227;T:435243137;N:14090 | 75 | 444383649 | 378084847 | 409250227 | 435243137 | 14090 | SRX28428341 | SRS24751214 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35885 | 35885 | SRR33167512 | SRX28428340 | SRS24751213 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AX7 S12 | GSM8919396 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | GRC355 AX7 S12 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919396 | GSM8919396: GRC355 AX7 S12; Danio rerio; RNA Seq | GSM8919396 r1 | GSM8919396 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AX7_S12_R1_001.fastq.gz | fastq | 2140829850.0 | 28544398.0 | GSM8919396 r1 | 0:75 | A:573637456;C:487537967;G:542176673;T:537445946;N:31808 | 75 | 573637456 | 487537967 | 542176673 | 537445946 | 31808 | SRX28428340 | SRS24751213 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35886 | 35886 | SRR33167513 | SRX28428339 | SRS24751212 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AX4 S8 | GSM8919395 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | GRC355 AX4 S8 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919395 | GSM8919395: GRC355 AX4 S8; Danio rerio; RNA Seq | GSM8919395 r1 | GSM8919395 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AX4_S8_R1_001.fastq.gz | fastq | 1621849275.0 | 21624657.0 | GSM8919395 r1 | 0:75 | A:427004733;C:380545003;G:418850461;T:395425815;N:23263 | 75 | 427004733 | 380545003 | 418850461 | 395425815 | 23263 | SRX28428339 | SRS24751212 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35887 | 35887 | SRR33167514 | SRX28428338 | SRS24751210 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 3H L7.D707 | GSM8919421 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing | MB125 3H L7.D707 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1 | GSM8919421 | GSM8919421: MB125 3H L7.D707; Danio rerio; RNA Seq | GSM8919421 r1 | GSM8919421 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_3H_L7.D707_1.fastq.gz MB125_3H_L7.D707_2.fastq.gz | fastq fastq | 2507284134.0 | 24581217.0 | GSM8919421 r1 | 0:51 1:51 | A:606166191;C:629419207;G:624900622;T:646726697;N:71417 | 51 | 51 | 606166191 | 629419207 | 624900622 | 646726697 | 71417 | SRX28428338 | SRS24751210 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35888 | 35888 | SRR33167515 | SRX28428337 | SRS24751211 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 3G L7.D705 | GSM8919420 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing | MB125 3G L7.D705 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1 | GSM8919420 | GSM8919420: MB125 3G L7.D705; Danio rerio; RNA Seq | GSM8919420 r1 | GSM8919420 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_3G_L7.D705_1.fastq.gz MB125_3G_L7.D705_2.fastq.gz | fastq fastq | 2312886924.0 | 22675362.0 | GSM8919420 r1 | 0:51 1:51 | A:558808137;C:581346006;G:578068942;T:594600445;N:63394 | 51 | 51 | 558808137 | 581346006 | 578068942 | 594600445 | 63394 | SRX28428337 | SRS24751211 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35889 | 35889 | SRR33167516 | SRX28428336 | SRS24751209 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 3F L7.D706 | GSM8919419 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing | MB125 3F L7.D706 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1 | GSM8919419 | GSM8919419: MB125 3F L7.D706; Danio rerio; RNA Seq | GSM8919419 r1 | GSM8919419 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_3F_L7.D706_1.fastq.gz MB125_3F_L7.D706_2.fastq.gz | fastq fastq | 2752811598.0 | 26988349.0 | GSM8919419 r1 | 0:51 1:51 | A:667499048;C:689713749;G:683954270;T:711568265;N:76266 | 51 | 51 | 667499048 | 689713749 | 683954270 | 711568265 | 76266 | SRX28428336 | SRS24751209 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35890 | 35890 | SRR33167517 | SRX28428335 | SRS24751207 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AX3 S5 | GSM8919394 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | GRC355 AX3 S5 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919394 | GSM8919394: GRC355 AX3 S5; Danio rerio; RNA Seq | GSM8919394 r1 | GSM8919394 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AX3_S5_R1_001.fastq.gz | fastq | 2554087275.0 | 34054497.0 | GSM8919394 r1 | 0:75 | A:679572493;C:596662581;G:654676127;T:623138913;N:37161 | 75 | 679572493 | 596662581 | 654676127 | 623138913 | 37161 | SRX28428335 | SRS24751207 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35891 | 35891 | SRR33167518 | SRX28428334 | SRS24751208 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AX1 S2 | GSM8919393 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing | GRC355 AX1 S2 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf | GSM8919393 | GSM8919393: GRC355 AX1 S2; Danio rerio; RNA Seq | GSM8919393 r1 | GSM8919393 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AX1_S2_R1_001.fastq.gz | fastq | 2056328850.0 | 27417718.0 | GSM8919393 r1 | 0:75 | A:547609875;C:481406742;G:529530435;T:497753038;N:28760 | 75 | 547609875 | 481406742 | 529530435 | 497753038 | 28760 | SRX28428334 | SRS24751208 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35892 | 35892 | SRR33167519 | SRX28428333 | SRS24751206 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AC7 S7 | GSM8919392 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing | GRC355 AC7 S7 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2 | GSM8919392 | GSM8919392: GRC355 AC7 S7; Danio rerio; RNA Seq | GSM8919392 r1 | GSM8919392 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AC7_S7_R1_001.fastq.gz | fastq | 2227335150.0 | 29697802.0 | GSM8919392 r1 | 0:75 | A:600851630;C:506204586;G:559397063;T:560849750;N:32121 | 75 | 600851630 | 506204586 | 559397063 | 560849750 | 32121 | SRX28428333 | SRS24751206 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Multi-stage | Multi-stage | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35893 | 35893 | SRR33167520 | SRX28428332 | SRS24751204 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AC6 S11 | GSM8919391 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing | GRC355 AC6 S11 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2 | GSM8919391 | GSM8919391: GRC355 AC6 S11; Danio rerio; RNA Seq | GSM8919391 r1 | GSM8919391 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AC6_S11_R1_001.fastq.gz | fastq | 2585681925.0 | 34475759.0 | GSM8919391 r1 | 0:75 | A:689801171;C:608098568;G:666027069;T:621732490;N:22627 | 75 | 689801171 | 608098568 | 666027069 | 621732490 | 22627 | SRX28428332 | SRS24751204 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Multi-stage | Multi-stage | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35894 | 35894 | SRR33167521 | SRX28428331 | SRS24751205 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AC5 S14 | GSM8919390 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing | GRC355 AC5 S14 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2 | GSM8919390 | GSM8919390: GRC355 AC5 S14; Danio rerio; RNA Seq | GSM8919390 r1 | GSM8919390 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AC5_S14_R1_001.fastq.gz | fastq | 2494451250.0 | 33259350.0 | GSM8919390 r1 | 0:75 | A:663836714;C:570411156;G:619148577;T:641019188;N:35615 | 75 | 663836714 | 570411156 | 619148577 | 641019188 | 35615 | SRX28428331 | SRS24751205 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Multi-stage | Multi-stage | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35895 | 35895 | SRR33167522 | SRX28428330 | SRS24751203 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AC4 S16 | GSM8919389 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing | GRC355 AC4 S16 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2 | GSM8919389 | GSM8919389: GRC355 AC4 S16; Danio rerio; RNA Seq | GSM8919389 r1 | GSM8919389 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AC4_S16_R1_001.fastq.gz | fastq | 2318944500.0 | 30919260.0 | GSM8919389 r1 | 0:75 | A:622730628;C:558676778;G:600421168;T:537095873;N:20053 | 75 | 622730628 | 558676778 | 600421168 | 537095873 | 20053 | SRX28428330 | SRS24751203 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Multi-stage | Multi-stage | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35896 | 35896 | SRR33167523 | SRX28428329 | SRS24751201 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AC3 S10 | GSM8919388 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing | GRC355 AC3 S10 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2 | GSM8919388 | GSM8919388: GRC355 AC3 S10; Danio rerio; RNA Seq | GSM8919388 r1 | GSM8919388 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AC3_S10_R1_001.fastq.gz | fastq | 2294756475.0 | 30596753.0 | GSM8919388 r1 | 0:75 | A:602530943;C:536584842;G:585162453;T:570445286;N:32951 | 75 | 602530943 | 536584842 | 585162453 | 570445286 | 32951 | SRX28428329 | SRS24751201 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Multi-stage | Multi-stage | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35897 | 35897 | SRR33167524 | SRX28428328 | SRS24751202 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | GRC355 AC2 S1 | GSM8919387 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing | GRC355 AC2 S1 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2 | GSM8919387 | GSM8919387: GRC355 AC2 S1; Danio rerio; RNA Seq | GSM8919387 r1 | GSM8919387 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP579141 | GRC355_AC2_S1_R1_001.fastq.gz | fastq | 2339756250.0 | 31196750.0 | GSM8919387 r1 | 0:75 | A:612473749;C:554816637;G:611772519;T:560660557;N:32788 | 75 | 612473749 | 554816637 | 611772519 | 560660557 | 32788 | SRX28428328 | SRS24751202 | SRA2113523 | US EPA | US EPA | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Multi-stage | Multi-stage | Multi-tissue | Multi-system | ||||||||||||||||||||||||||
| 35898 | 35898 | SRR33167525 | SRX28428327 | SRS24751200 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 3C L7.D704 | GSM8919418 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing | MB125 3C L7.D704 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1 | GSM8919418 | GSM8919418: MB125 3C L7.D704; Danio rerio; RNA Seq | GSM8919418 r1 | GSM8919418 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_3C_L7.D704_1.fastq.gz MB125_3C_L7.D704_2.fastq.gz | fastq fastq | 2190157566.0 | 21472133.0 | GSM8919418 r1 | 0:51 1:51 | A:516553798;C:562413569;G:556139060;T:554989063;N:62076 | 51 | 51 | 516553798 | 562413569 | 556139060 | 554989063 | 62076 | SRX28428327 | SRS24751200 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||||||||
| 35899 | 35899 | SRR33167526 | SRX28428326 | SRS24751198 | SRP579141 | PRJNA1251588 | Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish | GSE294778 | Transcriptome Analysis | Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic conventionally colonized controls and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free conventionally colonized normal and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae. | MB125 3B L7.D703 | GSM8919417 | source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing | MB125 3B L7.D703 | For Experiment 1 basecall files were converted to FASTQ by bcl2fastq2 demultiplexed quality trimmed and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2 Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed respectively in Partek Flow v.8.0.19.0428; St. Louis MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples | pooled heads collected anterior to swim bladder of larval zebrafish | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1 | GSM8919417 | GSM8919417: MB125 3B L7.D703; Danio rerio; RNA Seq | GSM8919417 r1 | GSM8919417 | 1 | Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis LLC Morrisville NC USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham NC USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1 paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina San Diego California cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824 KAPA Biosystems Wilmington MA. Sample libraries were then normalized randomly pooled and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2 purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham NC USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from… | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP579141 | MB125_3B_L7.D703_1.fastq.gz MB125_3B_L7.D703_2.fastq.gz | fastq fastq | 2461970328.0 | 24136964.0 | GSM8919417 r1 | 0:51 1:51 | A:580053108;C:631261740;G:628153535;T:622435609;N:66336 | 51 | 51 | 580053108 | 631261740 | 628153535 | 622435609 | 66336 | SRX28428326 | SRS24751198 | SRA2113523 | US EPA | US EPA | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | United States | 2025-04-16 | Larval | Larval | Multi-tissue | Multi-system |
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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");;