run_metadata
596 rows where devstage_curation = "Larval" and experiment.library_selection = "Oligo-dT"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5879 | 5879 | ERR1759701 | ERX1826022 | ERS1474296 | ERP020578 | PRJEB18632 | RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | E-MTAB-5323 | Transcriptome Analysis | The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes. | ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323 | Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. | Sample2 | SAMEA27136168 | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute | ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2 | Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | E MTAB 5323:Sample2 s | Sample2 s | RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. | Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | Illumina MiSeq | ERP020578 | Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16 | mochizukis_lab_myl7_actn2tdEos_72h_01.fastq.gz | fastq | 448234901.0 | 6016977.0 | E MTAB 5323:Sample2 | 0:74.50 1:0 | A:118923409;C:100586009;G:99987046;T:126071553;N:2666884 | 74 | 0 | 118923409 | 100586009 | 99987046 | 126071553 | 2666884 | ERX1826022 | ERS1474296 | ERA776061 | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive | 1 | 0.88465 | 0.27583 | 0.75398 | 0.55917 | 75 | B | usable mapping rate | illumina | miseq | full_length | poly_a | nebnext | bulk | unknown | unknown | Japan | 2016-12-15 | Larval | Larval | Heart | Cardiovascular System | |||||||||||||||||||
| 5880 | 5880 | ERR1759702 | ERX1826022 | ERS1474296 | ERP020578 | PRJEB18632 | RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | E-MTAB-5323 | Transcriptome Analysis | The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes. | ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323 | Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. | Sample2 | SAMEA27136168 | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute | ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2 | Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | E MTAB 5323:Sample2 s | Sample2 s | RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. | Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | Illumina MiSeq | ERP020578 | Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16 | mochizukis_lab_myl7_actn2tdEos_72h_02.fastq.gz | fastq | 448116860.0 | 6016977.0 | E MTAB 5323:Sample2 1 | 0:0 1:74.48 | A:127811460;C:99875207;G:106561979;T:113792335;N:75879 | 0 | 74 | 127811460 | 99875207 | 106561979 | 113792335 | 75879 | ERX1826022 | ERS1474296 | ERA776061 | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive | 1 | 0.91589 | 0.2509 | 0.79005 | 0.54852 | 75 | B | usable mapping rate | illumina | miseq | full_length | poly_a | nebnext | bulk | unknown | unknown | Japan | 2016-12-15 | Larval | Larval | Heart | Cardiovascular System | |||||||||||||||||||
| 5881 | 5881 | ERR1759699 | ERX1826021 | ERS1474295 | ERP020578 | PRJEB18632 | RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | E-MTAB-5323 | Transcriptome Analysis | The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes. | ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323 | Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. | Sample1 | SAMEA27135418 | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute | ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1 | Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | E MTAB 5323:Sample1 s | Sample1 s | RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. | Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | Illumina MiSeq | ERP020578 | Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16 | mochizukis_lab_myl7_NLSmCherry_72h_01.fastq.gz | fastq | 766363334.0 | 10284347.0 | E MTAB 5323:Sample1 | 0:74.52 1:0 | A:201960096;C:174999154;G:173403690;T:211341998;N:4658396 | 74 | 0 | 201960096 | 174999154 | 173403690 | 211341998 | 4658396 | ERX1826021 | ERS1474295 | ERA776061 | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive | 1 | 0.86003 | 0.20554 | 0.76301 | 0.55753 | 74 | B | usable mapping rate | illumina | miseq | full_length | poly_a | nebnext | bulk | unknown | unknown | Japan | 2016-12-15 | Larval | Larval | Heart | Cardiovascular System | |||||||||||||||||||
| 5882 | 5882 | ERR1759700 | ERX1826021 | ERS1474295 | ERP020578 | PRJEB18632 | RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | E-MTAB-5323 | Transcriptome Analysis | The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes. | ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323 | Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. | Sample1 | SAMEA27135418 | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute | ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1 | Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | E MTAB 5323:Sample1 s | Sample1 s | RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs. | Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | Illumina MiSeq | ERP020578 | Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf | ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16 | mochizukis_lab_myl7_NLSmCHerry_72h_02.fastq.gz | fastq | 766251339.0 | 10284347.0 | E MTAB 5323:Sample1 1 | 0:0 1:74.51 | A:214234414;C:174215653;G:180382062;T:197361982;N:57228 | 0 | 74 | 214234414 | 174215653 | 180382062 | 197361982 | 57228 | ERX1826021 | ERS1474295 | ERA776061 | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive | Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive | 1 | 0.87766 | 0.21561 | 0.77477 | 0.53919 | 73 | B | usable mapping rate | illumina | miseq | full_length | poly_a | nebnext | bulk | unknown | unknown | Japan | 2016-12-15 | Larval | Larval | Heart | Cardiovascular System | |||||||||||||||||||
| 9361 | 9361 | ERR3011947 | ERX3014407 | ERS2994081 | ERP112907 | PRJEB30451 | Effects of anti androgenic compounds on zebrafish insulin mutants | E-MTAB-7283 | Transcriptome Analysis | Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants. | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Flutamide 2 | SAMEA5186582 | Max Planck Institute for Heart and Lung Research | ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186582|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 2|scientific name:Danio rerio|strain:ins bns102 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | E MTAB 7283:Flutamide 2 s | Flutamide 2 s | Effects of anti androgenic compounds on zebrafish insulin mutants | insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Experimental Factor: compound:flutamide|Experimental Factor: dose:10 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | ERP112907 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Teja_Flutamide_2_R1.fastq.gz | fastq | 1754963940.0 | 23552243.0 | E MTAB 7283:Flutamide 2 | 0:74.51 1:0 | A:455444321;C:410713896;G:385640226;T:503155736;N:9761 | 74 | 0 | 455444321 | 410713896 | 385640226 | 503155736 | 9761 | ERX3014407 | ERS2994081 | ERA1697296 | European Nucleotide Archive | European Nucleotide Archive | 1 | 0.94351 | 0.11595 | 0.67483 | 0.48762 | 73 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Unknown | 2018-12-18 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 9362 | 9362 | ERR3011946 | ERX3014406 | ERS2994080 | ERP112907 | PRJEB30451 | Effects of anti androgenic compounds on zebrafish insulin mutants | E-MTAB-7283 | Transcriptome Analysis | Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants. | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Flutamide 1 | SAMEA5186581 | Max Planck Institute for Heart and Lung Research | ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186581|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 1|scientific name:Danio rerio|strain:ins bns102 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | E MTAB 7283:Flutamide 1 s | Flutamide 1 s | Effects of anti androgenic compounds on zebrafish insulin mutants | insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Experimental Factor: compound:flutamide|Experimental Factor: dose:10 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | ERP112907 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Teja_Flutamide_1_R1.fastq.gz | fastq | 1631102863.0 | 21898245.0 | E MTAB 7283:Flutamide 1 | 0:74.49 1:0 | A:424378341;C:380806325;G:358128992;T:467779945;N:9260 | 74 | 0 | 424378341 | 380806325 | 358128992 | 467779945 | 9260 | ERX3014406 | ERS2994080 | ERA1697296 | European Nucleotide Archive | European Nucleotide Archive | 1 | 0.94332 | 0.11797 | 0.67596 | 0.48847 | 75 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Unknown | 2018-12-18 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 9363 | 9363 | ERR3011945 | ERX3014405 | ERS2994079 | ERP112907 | PRJEB30451 | Effects of anti androgenic compounds on zebrafish insulin mutants | E-MTAB-7283 | Transcriptome Analysis | Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants. | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | DMSO 2 | SAMEA5186580 | Max Planck Institute for Heart and Lung Research | ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186580|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 2|scientific name:Danio rerio|strain:ins bns102 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | E MTAB 7283:DMSO 2 s | DMSO 2 s | Effects of anti androgenic compounds on zebrafish insulin mutants | insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | ERP112907 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Teja_DMSO_2_R1.fastq.gz | fastq | 1811573293.0 | 24316929.0 | E MTAB 7283:DMSO 2 | 0:74.50 1:0 | A:470888315;C:423635861;G:396796840;T:520242179;N:10098 | 74 | 0 | 470888315 | 423635861 | 396796840 | 520242179 | 10098 | ERX3014405 | ERS2994079 | ERA1697296 | European Nucleotide Archive | European Nucleotide Archive | 1 | 0.94219 | 0.12305 | 0.67184 | 0.47704 | 75 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Unknown | 2018-12-18 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 9364 | 9364 | ERR3011944 | ERX3014404 | ERS2994078 | ERP112907 | PRJEB30451 | Effects of anti androgenic compounds on zebrafish insulin mutants | E-MTAB-7283 | Transcriptome Analysis | Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants. | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | DMSO 1 | SAMEA5186579 | Max Planck Institute for Heart and Lung Research | ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186579|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 1|scientific name:Danio rerio|strain:ins bns102 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | E MTAB 7283:DMSO 1 s | DMSO 1 s | Effects of anti androgenic compounds on zebrafish insulin mutants | insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | ERP112907 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Teja_DMSO_1_R1.fastq.gz | fastq | 1609807409.0 | 21611475.0 | E MTAB 7283:DMSO 1 | 0:74.49 1:0 | A:420253680;C:374436301;G:352526427;T:462581933;N:9068 | 74 | 0 | 420253680 | 374436301 | 352526427 | 462581933 | 9068 | ERX3014404 | ERS2994078 | ERA1697296 | European Nucleotide Archive | European Nucleotide Archive | 1 | 0.94094 | 0.12292 | 0.67006 | 0.48442 | 75 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Unknown | 2018-12-18 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 9365 | 9365 | ERR3011943 | ERX3014403 | ERS2994077 | ERP112907 | PRJEB30451 | Effects of anti androgenic compounds on zebrafish insulin mutants | E-MTAB-7283 | Transcriptome Analysis | Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants. | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Cyproter1 2 | SAMEA5186578 | Max Planck Institute for Heart and Lung Research | ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186578|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Cyproter1 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Cyproter1 2|scientific name:Danio rerio|strain:ins bns102 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | E MTAB 7283:Cyproterone 2 s | Cyproterone 2 s | Effects of anti androgenic compounds on zebrafish insulin mutants | insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Experimental Factor: compound:cyproter1|Experimental Factor: dose:10 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | ERP112907 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Teja_Cyproterone_2_R1.fastq.gz | fastq | 1823142918.0 | 24468337.0 | E MTAB 7283:Cyproterone 2 | 0:74.51 1:0 | A:469387174;C:428783310;G:403791044;T:521171021;N:10369 | 74 | 0 | 469387174 | 428783310 | 403791044 | 521171021 | 10369 | ERX3014403 | ERS2994077 | ERA1697296 | European Nucleotide Archive | European Nucleotide Archive | 1 | 0.9432 | 0.11718 | 0.67389 | 0.4768 | 74 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Unknown | 2018-12-18 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 9366 | 9366 | ERR3011942 | ERX3014402 | ERS2994076 | ERP112907 | PRJEB30451 | Effects of anti androgenic compounds on zebrafish insulin mutants | E-MTAB-7283 | Transcriptome Analysis | Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants. | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Cyproter1 1 | SAMEA5186577 | Max Planck Institute for Heart and Lung Research | ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186577|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Cyproter1 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Cyproter1 1|scientific name:Danio rerio|strain:ins bns102 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | E MTAB 7283:Cyproterone 1 s | Cyproterone 1 s | Effects of anti androgenic compounds on zebrafish insulin mutants | insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina | Experimental Factor: compound:cyproter1|Experimental Factor: dose:10 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | ERP112907 | NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants | ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18 | Teja_Cyproterone_1_R1.fastq.gz | fastq | 1901027130.0 | 25512731.0 | E MTAB 7283:Cyproterone 1 | 0:74.51 1:0 | A:487302419;C:449208827;G:422183780;T:542321577;N:10527 | 74 | 0 | 487302419 | 449208827 | 422183780 | 542321577 | 10527 | ERX3014402 | ERS2994076 | ERA1697296 | European Nucleotide Archive | European Nucleotide Archive | 1 | 0.94427 | 0.11318 | 0.67294 | 0.47183 | 75 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Unknown | 2018-12-18 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 9951 | 9951 | ERR5961093 | ERX5601614 | ERS6490233 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae uninjected controls from the same batch. | Uninjected2 | Uninjected2 | ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8 | ERX5601614 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||||||||||||
| 9952 | 9952 | ERR5961092 | ERX5601613 | ERS6490232 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae uninjected controls from the same batch. | Uninjected1 | SAMEA8805898 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 06 23|ENA last update:2021 06 23|External Id:SAMEA8805898|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 06 23T08:18:31Z|INSDC last update:2021 06 23T08:18:31Z|INSDC status:public|Submitter Id:Uninjected1|common name:zebrafish|sample name:Uninjected1 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 06 23|ENA LAST UPDATE:2021 06 23 | WT1_R1_001.fastq WT1_R2_001.fastq | fastq fastq | 5664550800.0 | 18881836.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7 | 0:150 1:150 | A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763 | 150 | 150 | 1493322675 | 1337347146 | 1388414458 | 1444981758 | 484763 | ERX5601613 | ERS6490232 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95769 | 0.95822 | 0.04407 | 0.04391 | 0.69934 | 0.69958 | 0.4411 | 0.45319 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9953 | 9953 | ERR5961096 | ERX5601617 | ERS6490236 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae uninjected controls from the an additional batch. | Uninjected5 | SAMEA8805902 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805902|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected5|common name:zebrafish|sample name:Uninjected5 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | WT5_R1_001.fastq.gz WT5_R2_001.fastq.gz | fastq fastq | 9088444200.0 | 30294814.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 | 0:150 1:150 | A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622 | 150 | 150 | 2404715160 | 2098546919 | 2330441921 | 2254532578 | 207622 | ERX5601617 | ERS6490236 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95076 | 0.93857 | 0.06296 | 0.06222 | 0.68485 | 0.70047 | 0.47429 | 0.48524 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9954 | 9954 | ERR5961095 | ERX5601616 | ERS6490235 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae uninjected controls from the an additional batch. | Uninjected4 | SAMEA8805901 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805901|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected4|common name:zebrafish|sample name:Uninjected4 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | WT4_R1_001.fastq.gz WT4_R2_001.fastq.gz | fastq fastq | 9222083700.0 | 30740279.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10 | 0:150 1:150 | A:2328864269;C:2117919914;G:2560286870;T:2214801519;N:211128 | 150 | 150 | 2328864269 | 2117919914 | 2560286870 | 2214801519 | 211128 | ERX5601616 | ERS6490235 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95124 | 0.92695 | 0.05122 | 0.05036 | 0.69118 | 0.70634 | 0.47769 | 0.47806 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9955 | 9955 | ERR5961094 | ERX5601615 | ERS6490234 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae uninjected controls from the an additional batch. | Uninjected3 | SAMEA8805900 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805900|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected3|common name:zebrafish|sample name:Uninjected3 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | WT3_R1_001.fastq.gz WT3_R2_001.fastq.gz | fastq fastq | 9088444200.0 | 30294814.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9 | 0:150 1:150 | A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622 | 150 | 150 | 2404715160 | 2098546919 | 2330441921 | 2254532578 | 207622 | ERX5601615 | ERS6490234 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95071 | 0.93855 | 0.06295 | 0.06183 | 0.68511 | 0.70065 | 0.47621 | 0.48573 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9956 | 9956 | ERR5961091 | ERX5601612 | ERS6490231 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. | Cas9enzyme3 | SAMEA8805897 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805897|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme3|common name:zebrafish|sample name:Cas9enzyme3 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | RNA3_R1_001.fastq RNA3_R2_001.fastq | fastq fastq | 5814764400.0 | 19382548.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6 | 0:150 1:150 | A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867 | 150 | 150 | 1550014255 | 1359566801 | 1419514658 | 1485169819 | 498867 | ERX5601612 | ERS6490231 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.96166 | 0.96182 | 0.04962 | 0.04954 | 0.68172 | 0.68144 | 0.45683 | 0.46611 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9957 | 9957 | ERR5961090 | ERX5601611 | ERS6490230 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. | Cas9enzyme2 | SAMEA8805896 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805896|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme2|common name:zebrafish|sample name:Cas9enzyme2 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | RNA2_R1_001.fastq RNA2_R2_001.fastq | fastq fastq | 5927606100.0 | 19758687.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5 | 0:150 1:150 | A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534 | 150 | 150 | 1579767222 | 1387675810 | 1439122138 | 1520529396 | 511534 | ERX5601611 | ERS6490230 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.96217 | 0.96214 | 0.05174 | 0.05176 | 0.67083 | 0.6716 | 0.46772 | 0.47128 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9958 | 9958 | ERR5961089 | ERX5601610 | ERS6490229 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. | Cas9enzyme1 | SAMEA8805895 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805895|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme1|common name:zebrafish|sample name:Cas9enzyme1 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | RNA1_R1_001.fastq RNA1_R2_001.fastq | fastq fastq | 5738133000.0 | 19127110.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4 | 0:150 1:150 | A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691 | 150 | 150 | 1530616107 | 1342298453 | 1401357126 | 1463360623 | 500691 | ERX5601610 | ERS6490229 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95709 | 0.9569 | 0.05132 | 0.05149 | 0.68771 | 0.68846 | 0.45988 | 0.47329 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9959 | 9959 | ERR5961088 | ERX5601609 | ERS6490228 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. | Cas9mRNA3 | SAMEA8805894 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805894|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA3|common name:zebrafish|sample name:Cas9mRNA3 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | PRO3_R1_001.fastq PRO3_R2_001.fastq | fastq fastq | 9635841900.0 | 32119473.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3 | 0:150 1:150 | A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911 | 150 | 150 | 2562857735 | 2253487693 | 2325345541 | 2493627020 | 523911 | ERX5601609 | ERS6490228 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95769 | 0.95696 | 0.05441 | 0.05397 | 0.67424 | 0.67407 | 0.46338 | 0.46444 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9960 | 9960 | ERR5961087 | ERX5601608 | ERS6490227 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. | Cas9mRNA2 | SAMEA8805893 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805893|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA2|common name:zebrafish|sample name:Cas9mRNA2 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 10 21 | PRO2_R1_001.fastq PRO2_R2_001.fastq | fastq fastq | 8990649900.0 | 29968833.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2 | 0:150 1:150 | A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619 | 150 | 150 | 2370044440 | 2140400380 | 2185347925 | 2294361536 | 495619 | ERX5601608 | ERS6490227 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95444 | 0.95397 | 0.05839 | 0.05842 | 0.67377 | 0.67207 | 0.48505 | 0.48043 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9961 | 9961 | ERR5961086 | ERX5601607 | ERS6490226 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. | Cas9mRNA1 | SAMEA8805892 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805892|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA1|common name:zebrafish|sample name:Cas9mRNA1 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | PRO1_R1_001.fastq PRO1_R2_001.fastq | fastq fastq | 8803789500.0 | 29345965.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1 | 0:150 1:150 | A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952 | 150 | 150 | 2318913314 | 2090675347 | 2149054140 | 2244296747 | 849952 | ERX5601607 | ERS6490226 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.954 | 0.9549 | 0.04652 | 0.04639 | 0.70806 | 0.71386 | 0.45393 | 0.44921 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9962 | 9962 | ERR4902960 | ERX4769932 | ERS5427208 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected. | CRISPR RNAseq | SAMEA7670216 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670216|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:12Z|INSDC status:public|Submitter Id:CRISPR RNAseq8|common name:zebrafish|sample name:CRISPR RNAseq8 | Illumina MiSeq paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina MiSeq | ERP123184 | Illumina MiSeq paired end sequencing | ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 | WT2_R1_001.fastq.gz WT2_R2_001.fastq.gz | fastq fastq | 7020700500.0 | 23402335.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8 | 0:150 1:150 | A:1879937256;C:1626166066;G:1693802223;T:1820178560;N:616395 | 150 | 150 | 1879937256 | 1626166066 | 1693802223 | 1820178560 | 616395 | ERX4769932 | ERS5427208 | ERA3183786 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.92352 | 0.92388 | 0.04778 | 0.04768 | 0.6924 | 0.69205 | 0.45557 | 0.45865 | 150 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9963 | 9963 | ERR4902959 | ERX4769931 | ERS5427206 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected. | CRISPR RNAseq | SAMEA7670214 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670214|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq7|common name:zebrafish|sample name:CRISPR RNAseq7 | Illumina MiSeq paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina MiSeq | ERP123184 | Illumina MiSeq paired end sequencing | ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 | WT1_R1_001.fastq.gz WT1_R2_001.fastq.gz | fastq fastq | 5664550800.0 | 18881836.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7 | 0:150 1:150 | A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763 | 150 | 150 | 1493322675 | 1337347146 | 1388414458 | 1444981758 | 484763 | ERX4769931 | ERS5427206 | ERA3183786 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95767 | 0.95821 | 0.04411 | 0.04384 | 0.69944 | 0.69944 | 0.44168 | 0.45263 | 150 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9964 | 9964 | ERR4902958 | ERX4769930 | ERS5427204 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA. | CRISPR RNAseq | SAMEA7670212 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670212|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq6|common name:zebrafish|sample name:CRISPR RNAseq6 | Illumina MiSeq paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 6 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina MiSeq | ERP123184 | Illumina MiSeq paired end sequencing | ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 | RNA3_R1_001.fastq.gz RNA3_R2_001.fastq.gz | fastq fastq | 5814764400.0 | 19382548.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 6 | 0:150 1:150 | A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867 | 150 | 150 | 1550014255 | 1359566801 | 1419514658 | 1485169819 | 498867 | ERX4769930 | ERS5427204 | ERA3183786 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.96165 | 0.96177 | 0.04961 | 0.04952 | 0.68183 | 0.68142 | 0.45636 | 0.46565 | 150 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9965 | 9965 | ERR4902957 | ERX4769929 | ERS5427203 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA. | CRISPR RNAseq | SAMEA7670211 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670211|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq5|common name:zebrafish|sample name:CRISPR RNAseq5 | Illumina MiSeq paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 5 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina MiSeq | ERP123184 | Illumina MiSeq paired end sequencing | ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 | RNA2_R1_001.fastq.gz RNA2_R2_001.fastq.gz | fastq fastq | 5927606100.0 | 19758687.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 5 | 0:150 1:150 | A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534 | 150 | 150 | 1579767222 | 1387675810 | 1439122138 | 1520529396 | 511534 | ERX4769929 | ERS5427203 | ERA3183786 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.96212 | 0.96213 | 0.0519 | 0.05167 | 0.67099 | 0.6715 | 0.46875 | 0.47089 | 150 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9966 | 9966 | ERR4902956 | ERX4769928 | ERS5427201 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA. | CRISPR RNAseq | SAMEA7670209 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670209|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq4|common name:zebrafish|sample name:CRISPR RNAseq4 | Illumina MiSeq paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 4 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina MiSeq | ERP123184 | Illumina MiSeq paired end sequencing | ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 | RNA1_R1_001.fastq.gz RNA1_R2_001.fastq.gz | fastq fastq | 5738133000.0 | 19127110.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 4 | 0:150 1:150 | A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691 | 150 | 150 | 1530616107 | 1342298453 | 1401357126 | 1463360623 | 500691 | ERX4769928 | ERS5427201 | ERA3183786 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95706 | 0.9569 | 0.05122 | 0.05151 | 0.68757 | 0.68822 | 0.46039 | 0.4732 | 150 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9967 | 9967 | ERR4902955 | ERX4769927 | ERS5427199 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme. | CRISPR RNAseq | SAMEA7670207 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670207|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq3|common name:zebrafish|sample name:CRISPR RNAseq3 | Illumina MiSeq paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 3 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina MiSeq | ERP123184 | Illumina MiSeq paired end sequencing | ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 | PRO3_R1_001.fastq.gz PRO3_R2_001.fastq.gz | fastq fastq | 9635841900.0 | 32119473.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 3 | 0:150 1:150 | A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911 | 150 | 150 | 2562857735 | 2253487693 | 2325345541 | 2493627020 | 523911 | ERX4769927 | ERS5427199 | ERA3183786 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95766 | 0.95695 | 0.05445 | 0.05404 | 0.67432 | 0.67403 | 0.46385 | 0.46442 | 150 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9968 | 9968 | ERR4902954 | ERX4769926 | ERS5427197 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme. | CRISPR RNAseq | SAMEA7670205 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670205|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq2|common name:zebrafish|sample name:CRISPR RNAseq2 | Illumina MiSeq paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 2 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina MiSeq | ERP123184 | Illumina MiSeq paired end sequencing | ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 | PRO2_R1_001.fastq.gz PRO2_R2_001.fastq.gz | fastq fastq | 8990649900.0 | 29968833.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 2 | 0:150 1:150 | A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619 | 150 | 150 | 2370044440 | 2140400380 | 2185347925 | 2294361536 | 495619 | ERX4769926 | ERS5427197 | ERA3183786 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95444 | 0.95393 | 0.05848 | 0.05894 | 0.67438 | 0.67255 | 0.4825 | 0.48028 | 150 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 9969 | 9969 | ERR4902953 | ERX4769925 | ERS5427195 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme. | CRISPR RNAseq | SAMEA7670203 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670203|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq1|common name:zebrafish|sample name:CRISPR RNAseq1 | Illumina MiSeq paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 1 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina MiSeq | ERP123184 | Illumina MiSeq paired end sequencing | ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 | PRO1_R1_001.fastq.gz PRO1_R2_001.fastq.gz | fastq fastq | 8803789500.0 | 29345965.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 1 | 0:150 1:150 | A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952 | 150 | 150 | 2318913314 | 2090675347 | 2149054140 | 2244296747 | 849952 | ERX4769925 | ERS5427195 | ERA3183786 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95403 | 0.95489 | 0.04655 | 0.0464 | 0.70816 | 0.71403 | 0.45357 | 0.44874 | 150 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||
| 10155 | 10155 | ERR5236196 | ERX5039563 | ERS5672247 | ERP126773 | PRJEB42852 | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E-MTAB-10068 | Transcriptome Analysis | Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Zebrafish WT 3 | SAMEA7984965 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA | ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984965|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 3 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E MTAB 10068:Zebrafish WT 3 p | Zebrafish WT 3 p | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP126773 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Zebrafish_WT_3_1.fastq.gz Zebrafish_WT_3_2.fastq.gz | fastq fastq | 7150981594.0 | 23678747.0 | E MTAB 10068:Zebrafish WT 3 | 0:151 1:151 | A:1885053833;C:1690814929;G:1772259046;T:1802798453;N:55333 | 151 | 151 | 1885053833 | 1690814929 | 1772259046 | 1802798453 | 55333 | ERX5039563 | ERS5672247 | ERA3400155 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | 2 | 0.95124 | 0.95221 | 0.08338 | 0.08285 | 0.69181 | 0.69256 | 0.46157 | 0.46139 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2022-01-26 | Larval | Larval | Eye | Sensory System | |||||||||||||
| 10156 | 10156 | ERR5236195 | ERX5039562 | ERS5672246 | ERP126773 | PRJEB42852 | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E-MTAB-10068 | Transcriptome Analysis | Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Zebrafish WT 2 | SAMEA7984964 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA | ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984964|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 2 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E MTAB 10068:Zebrafish WT 2 p | Zebrafish WT 2 p | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP126773 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Zebrafish_WT_2_1.fastq.gz Zebrafish_WT_2_2.fastq.gz | fastq fastq | 7214044026.0 | 23887563.0 | E MTAB 10068:Zebrafish WT 2 | 0:151 1:151 | A:1902219751;C:1705162605;G:1795933407;T:1810669383;N:58880 | 151 | 151 | 1902219751 | 1705162605 | 1795933407 | 1810669383 | 58880 | ERX5039562 | ERS5672246 | ERA3400155 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | 2 | 0.95311 | 0.95386 | 0.07898 | 0.07845 | 0.69045 | 0.69061 | 0.46066 | 0.4628 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2022-01-26 | Larval | Larval | Eye | Sensory System | |||||||||||||
| 10157 | 10157 | ERR5236194 | ERX5039561 | ERS5672245 | ERP126773 | PRJEB42852 | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E-MTAB-10068 | Transcriptome Analysis | Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Zebrafish WT 1 | SAMEA7984963 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA | ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984963|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 1 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E MTAB 10068:Zebrafish WT 1 p | Zebrafish WT 1 p | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP126773 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Zebrafish_WT_1_1.fastq.gz Zebrafish_WT_1_2.fastq.gz | fastq fastq | 6632043216.0 | 21960408.0 | E MTAB 10068:Zebrafish WT 1 | 0:151 1:151 | A:1763732625;C:1547925091;G:1636588945;T:1683739270;N:57285 | 151 | 151 | 1763732625 | 1547925091 | 1636588945 | 1683739270 | 57285 | ERX5039561 | ERS5672245 | ERA3400155 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | 2 | 0.9495 | 0.95025 | 0.08958 | 0.08856 | 0.68661 | 0.68598 | 0.46029 | 0.46171 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2022-01-26 | Larval | Larval | Eye | Sensory System | |||||||||||||
| 10158 | 10158 | ERR5236193 | ERX5039560 | ERS5672244 | ERP126773 | PRJEB42852 | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E-MTAB-10068 | Transcriptome Analysis | Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Zebrafish mab21l1 3 | SAMEA7984962 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA | ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984962|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 3 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E MTAB 10068:Zebrafish mab21l1 3 p | Zebrafish mab21l1 3 p | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Experimental Factor: genotype:homozygous mab21l1 c.107delA | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP126773 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Zebrafish_mab21l1_3_1.fastq.gz Zebrafish_mab21l1_3_2.fastq.gz | fastq fastq | 6182833618.0 | 20472959.0 | E MTAB 10068:Zebrafish mab21l1 3 | 0:151 1:151 | A:1613191835;C:1471874932;G:1547131522;T:1550575662;N:59667 | 151 | 151 | 1613191835 | 1471874932 | 1547131522 | 1550575662 | 59667 | ERX5039560 | ERS5672244 | ERA3400155 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | 2 | 0.95645 | 0.95788 | 0.0697 | 0.06969 | 0.70096 | 0.70033 | 0.43342 | 0.43242 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2022-01-26 | Larval | Larval | Eye | Sensory System | |||||||||||||
| 10159 | 10159 | ERR5236192 | ERX5039559 | ERS5672243 | ERP126773 | PRJEB42852 | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E-MTAB-10068 | Transcriptome Analysis | Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Zebrafish mab21l1 2 | SAMEA7984961 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA | ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984961|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 2 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E MTAB 10068:Zebrafish mab21l1 2 p | Zebrafish mab21l1 2 p | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Experimental Factor: genotype:homozygous mab21l1 c.107delA | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP126773 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Zebrafish_mab21l1_2_1.fastq.gz Zebrafish_mab21l1_2_2.fastq.gz | fastq fastq | 6989382602.0 | 23143651.0 | E MTAB 10068:Zebrafish mab21l1 2 | 0:151 1:151 | A:1841093814;C:1660652130;G:1754262273;T:1733319973;N:54412 | 151 | 151 | 1841093814 | 1660652130 | 1754262273 | 1733319973 | 54412 | ERX5039559 | ERS5672243 | ERA3400155 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | 2 | 0.95595 | 0.95712 | 0.07199 | 0.07107 | 0.70485 | 0.70431 | 0.42033 | 0.42681 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2022-01-26 | Larval | Larval | Eye | Sensory System | |||||||||||||
| 10160 | 10160 | ERR5236191 | ERX5039558 | ERS5672242 | ERP126773 | PRJEB42852 | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E-MTAB-10068 | Transcriptome Analysis | Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Zebrafish mab21l1 1 | SAMEA7984960 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA | ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984960|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 1 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | E MTAB 10068:Zebrafish mab21l1 1 p | Zebrafish mab21l1 1 p | RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. | Experimental Factor: genotype:homozygous mab21l1 c.107delA | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP126773 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf | ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 | Zebrafish_mab21l1_1_1.fastq.gz Zebrafish_mab21l1_1_2.fastq.gz | fastq fastq | 6882371922.0 | 22789311.0 | E MTAB 10068:Zebrafish mab21l1 1 | 0:151 1:151 | A:1803380739;C:1630414039;G:1732263332;T:1716255495;N:58317 | 151 | 151 | 1803380739 | 1630414039 | 1732263332 | 1716255495 | 58317 | ERX5039558 | ERS5672242 | ERA3400155 | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive | 2 | 0.95518 | 0.95612 | 0.07088 | 0.07032 | 0.70526 | 0.70457 | 0.42942 | 0.4302 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2022-01-26 | Larval | Larval | Eye | Sensory System | |||||||||||||
| 10176 | 10176 | ERR5858457 | ERX5504346 | ERS6343450 | ERP128749 | PRJEB44676 | scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord | E-MTAB-10390 | Transcriptome Analysis | To analyse lesion induced gene regulation in progenitor cells at single cell resolution we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals. | ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24 | Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines. | Naive | SAMEA8658904 | University Of Edinburgh | ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658904|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Naive|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|organism part:spinal cord|sample name:E MTAB 10390:Naive|sex:mixed|strain:WIK | Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord | E MTAB 10390:Naive p | Naive p | scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord | Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines. | Experimental Factor: injury:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP128749 | Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord | ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24 | Naive.bam | bam | 44972162730.0 | 499690697.0 | E MTAB 10390:Naive | 0:90 | A:13658826375;C:8733304343;G:9348137569;T:13228064343;N:3830100 | 90 | 13658826375 | 8733304343 | 9348137569 | 13228064343 | 3830100 | ERX5504346 | ERS6343450 | ERA4142789 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 1 | 0.89428 | 0.32693 | 0.75276 | 0.5314 | 90 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2021-05-24 | Larval | Larval | Spinal Cord | Nervous System | ||||||||||||||||||||
| 10177 | 10177 | ERR5858456 | ERX5504345 | ERS6343449 | ERP128749 | PRJEB44676 | scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord | E-MTAB-10390 | Transcriptome Analysis | To analyse lesion induced gene regulation in progenitor cells at single cell resolution we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals. | ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24 | Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines. | Lesi1d | SAMEA8658903 | University Of Edinburgh | ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658903|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Lesi1d|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|injury:spinal injury lesion|organism part:spinal cord|sample name:E MTAB 10390:Lesi1d|sex:mixed|strain:WIK | Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord | E MTAB 10390:Lesioned p | Lesioned p | scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord | Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines. | Experimental Factor: injury:spinal injury lesion | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP128749 | Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord | ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24 | Lesioned.bam | bam | 49902588630.0 | 554473207.0 | E MTAB 10390:Lesioned | 0:90 | A:14713351178;C:10191139050;G:10897887675;T:14095967201;N:4243526 | 90 | 14713351178 | 10191139050 | 10897887675 | 14095967201 | 4243526 | ERX5504345 | ERS6343449 | ERA4142789 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 1 | 0.91197 | 0.29137 | 0.7568 | 0.56523 | 90 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2021-05-24 | Larval | Larval | Spinal Cord | Nervous System | ||||||||||||||||||||
| 10186 | 10186 | ERR6212423 | ERX5847531 | ERS7094943 | ERP130388 | PRJEB46176 | scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord | E-MTAB-10379_3 | Transcriptome Analysis | To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals. | ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08 | Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines | Naive | SAMEA9361876 | University Of Edinburgh | ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK | Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord | E MTAB 10379 3:Naive p | Naive p | scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord | Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines | Experimental Factor: injury:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP130388 | Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord | ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08 | Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz | fastq fastq fastq | 60168324125.0 | 481346593.0 | E MTAB 10379 3:Naive | 0:8 1:27 2:90 | A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241 | 8 | 27 | 90 | 12424400694 | 9366563781 | 10029312355 | 11497237299 | 3679241 | ERX5847531 | ERS7094943 | ERA5186263 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 1 | 0.94834 | 0.09482 | 0.802 | 0.5277 | 90 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2021-07-08 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||
| 10187 | 10187 | ERR6212422 | ERX5847530 | ERS7094942 | ERP130388 | PRJEB46176 | scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord | E-MTAB-10379_3 | Transcriptome Analysis | To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals. | ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08 | Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines | Lesi1d | SAMEA9361875 | University Of Edinburgh | ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK | Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord | E MTAB 10379 3:Lesioned p | Lesioned p | scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord | Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines | Experimental Factor: injury:spinal cord lesion | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP130388 | Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord | ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08 | Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz | fastq fastq fastq | 61701873000.0 | 493614984.0 | E MTAB 10379 3:Lesioned | 0:8 1:27 2:90 | A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277 | 8 | 27 | 90 | 12952533019 | 9222397450 | 9920185920 | 12326470894 | 3761277 | ERX5847530 | ERS7094942 | ERA5186263 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 1 | 0.93082 | 0.10862 | 0.80302 | 0.54924 | 90 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2021-07-08 | Larval | Larval | Multi-tissue | Multi-system | ||||||||||||||||||
| 11047 | 11047 | ERR10476807 | ERX9997150 | ERS13672475 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day6 | SAMEA111562619 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d6 1|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star pos d6 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:183 283033 | Sample 0256 076 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_076_FR_NSP_TR1_SL1_S7_L001_R1_001-pooled.fastq.gz 0256_076_FR_NSP_TR1_SL1_S7_L001_R2_001-pooled.fastq.gz | fastq fastq | 2974117224.0 | 29158012.0 | ena RUN TAB 09 11 2022 11:52:59:183 283034 | 0:51 1:51 | A:816102587;C:662715848;G:672777315;T:822487687;N:33787 | 51 | 51 | 816102587 | 662715848 | 672777315 | 822487687 | 33787 | ERX9997150 | ERS13672475 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11050 | 11050 | ERR10476814 | ERX9997157 | ERS13672482 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day13 | SAMEA111562626 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d13 3|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star pos d13 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:186 283047 | Sample 0256 083 FR NSP TR2 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_083_FR_NSP_TR2_SL1_S14_L001_R1_001-pooled.fastq.gz 0256_083_FR_NSP_TR2_SL1_S14_L001_R2_001-pooled.fastq.gz | fastq fastq | 5492667156.0 | 53849678.0 | ena RUN TAB 09 11 2022 11:52:59:186 283048 | 0:51 1:51 | A:1546610275;C:1178241230;G:1195797489;T:1571955787;N:62375 | 51 | 51 | 1546610275 | 1178241230 | 1195797489 | 1571955787 | 62375 | ERX9997157 | ERS13672482 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11051 | 11051 | ERR10476829 | ERX9997172 | ERS13672497 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day6 | SAMEA111562641 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d6 3|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star neg d6 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:192 283077 | Sample 0256 103 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_103_FR_NSP_TR1_SL1_S32_L001_R1_001-pooled.fastq.gz 0256_103_FR_NSP_TR1_SL1_S32_L001_R2_001-pooled.fastq.gz | fastq fastq | 3120070248.0 | 30588924.0 | ena RUN TAB 09 11 2022 11:52:59:193 283078 | 0:51 1:51 | A:846274026;C:707353227;G:707836608;T:858570820;N:35567 | 51 | 51 | 846274026 | 707353227 | 707836608 | 858570820 | 35567 | ERX9997172 | ERS13672497 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11053 | 11053 | ERR10476796 | ERX9997139 | ERS13672464 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day13 | SAMEA111562608 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d13 5|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:tu wt d13 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:178 283011 | Sample 0256 010 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_010_FR_NSP_TR1_SL1_S21_L001_R1_001-pooled.fastq.gz 0256_010_FR_NSP_TR1_SL1_S21_L001_R2_001-pooled.fastq.gz | fastq fastq | 2969687772.0 | 29114586.0 | ena RUN TAB 09 11 2022 11:52:59:179 283012 | 0:51 1:51 | A:762435544;C:713336460;G:731717998;T:762096042;N:101728 | 51 | 51 | 762435544 | 713336460 | 731717998 | 762096042 | 101728 | ERX9997139 | ERS13672464 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11055 | 11055 | ERR10476836 | ERX9997179 | ERS13672504 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day13 | SAMEA111562648 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d13 5|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star neg d13 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:195 283091 | Sample 0256 110 FR NSP TR2 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_110_FR_NSP_TR2_SL1_S39_L001_R1_001-pooled.fastq.gz 0256_110_FR_NSP_TR2_SL1_S39_L001_R2_001-pooled.fastq.gz | fastq fastq | 2758547160.0 | 27044580.0 | ena RUN TAB 09 11 2022 11:52:59:196 283092 | 0:51 1:51 | A:732517446;C:640766914;G:643632251;T:741598802;N:31747 | 51 | 51 | 732517446 | 640766914 | 643632251 | 741598802 | 31747 | ERX9997179 | ERS13672504 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11056 | 11056 | ERR10476808 | ERX9997151 | ERS13672476 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day6 | SAMEA111562620 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d6 2|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star pos d6 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:184 283035 | Sample 0256 077 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_077_FR_NSP_TR1_SL1_S8_L001_R1_001-pooled.fastq.gz 0256_077_FR_NSP_TR1_SL1_S8_L001_R2_001-pooled.fastq.gz | fastq fastq | 3595088328.0 | 35245964.0 | ena RUN TAB 09 11 2022 11:52:59:184 283036 | 0:51 1:51 | A:985480827;C:803117311;G:811895458;T:994553698;N:41034 | 51 | 51 | 985480827 | 803117311 | 811895458 | 994553698 | 41034 | ERX9997151 | ERS13672476 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11058 | 11058 | ERR10476827 | ERX9997170 | ERS13672495 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day6 | SAMEA111562639 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d6 1|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star neg d6 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:192 283073 | Sample 0256 101 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_101_FR_NSP_TR1_SL1_S30_L001_R1_001-pooled.fastq.gz 0256_101_FR_NSP_TR1_SL1_S30_L001_R2_001-pooled.fastq.gz | fastq fastq | 3504125952.0 | 34354176.0 | ena RUN TAB 09 11 2022 11:52:59:192 283074 | 0:51 1:51 | A:947138693;C:797358353;G:798903844;T:960685108;N:39954 | 51 | 51 | 947138693 | 797358353 | 798903844 | 960685108 | 39954 | ERX9997170 | ERS13672495 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11060 | 11060 | ERR10476794 | ERX9997137 | ERS13672462 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day13 | SAMEA111562606 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d13 3|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:tu wt d13 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:178 283007 | Sample 0256 008 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_008_FR_NSP_TR1_SL1_S1_L001_R1_001-pooled.fastq.gz 0256_008_FR_NSP_TR1_SL1_S1_L001_R2_001-pooled.fastq.gz | fastq fastq | 2659023618.0 | 26068859.0 | ena RUN TAB 09 11 2022 11:52:59:178 283008 | 0:51 1:51 | A:670947753;C:637136773;G:677570266;T:673338670;N:30156 | 51 | 51 | 670947753 | 637136773 | 677570266 | 673338670 | 30156 | ERX9997137 | ERS13672462 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11061 | 11061 | ERR10476833 | ERX9997176 | ERS13672501 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day13 | SAMEA111562645 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d13 2|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star neg d13 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:194 283085 | Sample 0256 107 FR NSP TR2 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_107_FR_NSP_TR2_SL1_S36_L001_R1_001-pooled.fastq.gz 0256_107_FR_NSP_TR2_SL1_S36_L001_R2_001-pooled.fastq.gz | fastq fastq | 3282322362.0 | 32179631.0 | ena RUN TAB 09 11 2022 11:52:59:194 283086 | 0:51 1:51 | A:898607442;C:734331926;G:739939203;T:909406172;N:37619 | 51 | 51 | 898607442 | 734331926 | 739939203 | 909406172 | 37619 | ERX9997176 | ERS13672501 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11063 | 11063 | ERR10476828 | ERX9997171 | ERS13672496 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day6 | SAMEA111562640 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d6 2|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star neg d6 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:192 283075 | Sample 0256 102 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_102_FR_NSP_TR1_SL1_S31_L001_R1_001-pooled.fastq.gz 0256_102_FR_NSP_TR1_SL1_S31_L001_R2_001-pooled.fastq.gz | fastq fastq | 3969901404.0 | 38920602.0 | ena RUN TAB 09 11 2022 11:52:59:192 283076 | 0:51 1:51 | A:1079447747;C:894502841;G:908706945;T:1087198510;N:45361 | 51 | 51 | 1079447747 | 894502841 | 908706945 | 1087198510 | 45361 | ERX9997171 | ERS13672496 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11068 | 11068 | ERR10476790 | ERX9997133 | ERS13672458 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day6 | SAMEA111562602 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d6 4|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:tu wt d6 4|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:176 282999 | Sample 0256 004 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_004_FR_NSP_TR1_SL1_S16_L001_R1_001-pooled.fastq.gz 0256_004_FR_NSP_TR1_SL1_S16_L001_R2_001-pooled.fastq.gz | fastq fastq | 2693489520.0 | 26406760.0 | ena RUN TAB 09 11 2022 11:52:59:176 283000 | 0:51 1:51 | A:701762127;C:639663261;G:643729664;T:708242984;N:91484 | 51 | 51 | 701762127 | 639663261 | 643729664 | 708242984 | 91484 | ERX9997133 | ERS13672458 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11070 | 11070 | ERR10476791 | ERX9997134 | ERS13672459 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day6 | SAMEA111562603 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d6 5|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:tu wt d6 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:176 283001 | Sample 0256 005 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_005_FR_NSP_TR1_SL1_S17_L001_R1_001-pooled.fastq.gz 0256_005_FR_NSP_TR1_SL1_S17_L001_R2_001-pooled.fastq.gz | fastq fastq | 2904430620.0 | 28474810.0 | ena RUN TAB 09 11 2022 11:52:59:176 283002 | 0:51 1:51 | A:777892611;C:666758312;G:672026589;T:787654140;N:98968 | 51 | 51 | 777892611 | 666758312 | 672026589 | 787654140 | 98968 | ERX9997134 | ERS13672459 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11074 | 11074 | ERR10476788 | ERX9997131 | ERS13672456 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day6 | SAMEA111562600 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d6 2|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:tu wt d6 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:175 282995 | Sample 0256 002 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_002_FR_NSP_TR1_SL1_S14_L001_R1_001-pooled.fastq.gz 0256_002_FR_NSP_TR1_SL1_S14_L001_R2_001-pooled.fastq.gz | fastq fastq | 2385303456.0 | 23385328.0 | ena RUN TAB 09 11 2022 11:52:59:175 282996 | 0:51 1:51 | A:620601269;C:567608030;G:568555174;T:628457831;N:81152 | 51 | 51 | 620601269 | 567608030 | 568555174 | 628457831 | 81152 | ERX9997131 | ERS13672456 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11077 | 11077 | ERR10476816 | ERX9997159 | ERS13672484 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day13 | SAMEA111562628 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d13 5|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star pos d13 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:187 283051 | Sample 0256 085 FR NSP TRP SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_085_FR_NSP_TRP_SL1_S16_L001_R1_001-pooled.fastq.gz 0256_085_FR_NSP_TRP_SL1_S16_L001_R2_001-pooled.fastq.gz | fastq fastq | 3264856596.0 | 32008398.0 | ena RUN TAB 09 11 2022 11:52:59:187 283052 | 0:51 1:51 | A:908889213;C:708892816;G:727180747;T:919857088;N:36732 | 51 | 51 | 908889213 | 708892816 | 727180747 | 919857088 | 36732 | ERX9997159 | ERS13672484 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11078 | 11078 | ERR10476813 | ERX9997156 | ERS13672481 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day13 | SAMEA111562625 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d13 2|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star pos d13 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:186 283045 | Sample 0256 082 FR NSP TR2 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_082_FR_NSP_TR2_SL1_S13_L001_R1_001-pooled.fastq.gz 0256_082_FR_NSP_TR2_SL1_S13_L001_R2_001-pooled.fastq.gz | fastq fastq | 3037654248.0 | 29780924.0 | ena RUN TAB 09 11 2022 11:52:59:186 283046 | 0:51 1:51 | A:859112641;C:645943863;G:660257800;T:872305592;N:34352 | 51 | 51 | 859112641 | 645943863 | 660257800 | 872305592 | 34352 | ERX9997156 | ERS13672481 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11079 | 11079 | ERR10476832 | ERX9997175 | ERS13672500 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day13 | SAMEA111562644 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d13 1|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star neg d13 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:194 283083 | Sample 0256 106 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_106_FR_NSP_TR1_SL1_S35_L001_R1_001-pooled.fastq.gz 0256_106_FR_NSP_TR1_SL1_S35_L001_R2_001-pooled.fastq.gz | fastq fastq | 2761703040.0 | 27075520.0 | ena RUN TAB 09 11 2022 11:52:59:194 283084 | 0:51 1:51 | A:761065450;C:610246142;G:622228689;T:768131440;N:31319 | 51 | 51 | 761065450 | 610246142 | 622228689 | 768131440 | 31319 | ERX9997175 | ERS13672500 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11080 | 11080 | ERR10476810 | ERX9997153 | ERS13672478 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day6 | SAMEA111562622 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d6 4|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star pos d6 4|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:184 283039 | Sample 0256 079 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_079_FR_NSP_TR1_SL1_S10_L001_R1_001-pooled.fastq.gz 0256_079_FR_NSP_TR1_SL1_S10_L001_R2_001-pooled.fastq.gz | fastq fastq | 2745379674.0 | 26915487.0 | ena RUN TAB 09 11 2022 11:52:59:185 283040 | 0:51 1:51 | A:762974242;C:602287296;G:611894421;T:768192503;N:31212 | 51 | 51 | 762974242 | 602287296 | 611894421 | 768192503 | 31212 | ERX9997153 | ERS13672478 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11081 | 11081 | ERR10476811 | ERX9997154 | ERS13672479 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day6 | SAMEA111562623 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d6 5|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star pos d6 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:185 283041 | Sample 0256 080 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_080_FR_NSP_TR1_SL1_S11_L001_R1_001-pooled.fastq.gz 0256_080_FR_NSP_TR1_SL1_S11_L001_R2_001-pooled.fastq.gz | fastq fastq | 3212151870.0 | 31491685.0 | ena RUN TAB 09 11 2022 11:52:59:185 283042 | 0:51 1:51 | A:890500591;C:706313900;G:715518225;T:899782352;N:36802 | 51 | 51 | 890500591 | 706313900 | 715518225 | 899782352 | 36802 | ERX9997154 | ERS13672479 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11085 | 11085 | ERR10476809 | ERX9997152 | ERS13672477 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day6 | SAMEA111562621 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d6 3|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star pos d6 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:184 283037 | Sample 0256 078 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_078_FR_NSP_TR1_SL1_S9_L001_R1_001-pooled.fastq.gz 0256_078_FR_NSP_TR1_SL1_S9_L001_R2_001-pooled.fastq.gz | fastq fastq | 3412655106.0 | 33457403.0 | ena RUN TAB 09 11 2022 11:52:59:184 283038 | 0:51 1:51 | A:942783320;C:753155142;G:767154692;T:949522969;N:38983 | 51 | 51 | 942783320 | 753155142 | 767154692 | 949522969 | 38983 | ERX9997152 | ERS13672477 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11086 | 11086 | ERR10476789 | ERX9997132 | ERS13672457 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day6 | SAMEA111562601 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d6 3|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:tu wt d6 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:175 282997 | Sample 0256 003 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_003_FR_NSP_TR1_SL1_S15_L001_R1_001-pooled.fastq.gz 0256_003_FR_NSP_TR1_SL1_S15_L001_R2_001-pooled.fastq.gz | fastq fastq | 2999816634.0 | 29409967.0 | ena RUN TAB 09 11 2022 11:52:59:176 282998 | 0:51 1:51 | A:771170539;C:720448182;G:729961101;T:778133283;N:103529 | 51 | 51 | 771170539 | 720448182 | 729961101 | 778133283 | 103529 | ERX9997132 | ERS13672457 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11087 | 11087 | ERR10476830 | ERX9997173 | ERS13672498 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day6 | SAMEA111562642 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d6 4|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star neg d6 4|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:193 283079 | Sample 0256 104 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_104_FR_NSP_TR1_SL1_S33_L001_R1_001-pooled.fastq.gz 0256_104_FR_NSP_TR1_SL1_S33_L001_R2_001-pooled.fastq.gz | fastq fastq | 2943756210.0 | 28860355.0 | ena RUN TAB 09 11 2022 11:52:59:193 283080 | 0:51 1:51 | A:806343784;C:657990854;G:663721905;T:815666113;N:33554 | 51 | 51 | 806343784 | 657990854 | 663721905 | 815666113 | 33554 | ERX9997173 | ERS13672498 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11088 | 11088 | ERR10476835 | ERX9997178 | ERS13672503 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day13 | SAMEA111562647 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d13 4|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star neg d13 4|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:195 283089 | Sample 0256 109 FR NSP TR2 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_109_FR_NSP_TR2_SL1_S38_L001_R1_001-pooled.fastq.gz 0256_109_FR_NSP_TR2_SL1_S38_L001_R2_001-pooled.fastq.gz | fastq fastq | 3406677396.0 | 33398798.0 | ena RUN TAB 09 11 2022 11:52:59:195 283090 | 0:51 1:51 | A:928579532;C:768636951;G:771636154;T:937786376;N:38383 | 51 | 51 | 928579532 | 768636951 | 771636154 | 937786376 | 38383 | ERX9997178 | ERS13672503 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11090 | 11090 | ERR10476787 | ERX9997130 | ERS13672455 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day6 | SAMEA111562599 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d6 1|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:tu wt d6 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:174 282993 | Sample 0256 001 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_001_FR_NSP_TR1_SL1_S13_L001_R1_001-pooled.fastq.gz 0256_001_FR_NSP_TR1_SL1_S13_L001_R2_001-pooled.fastq.gz | fastq fastq | 2739613002.0 | 26858951.0 | ena RUN TAB 09 11 2022 11:52:59:174 282994 | 0:51 1:51 | A:716316048;C:647929778;G:649844718;T:725429229;N:93229 | 51 | 51 | 716316048 | 647929778 | 649844718 | 725429229 | 93229 | ERX9997130 | ERS13672455 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11091 | 11091 | ERR10476812 | ERX9997155 | ERS13672480 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day13 | SAMEA111562624 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d13 1|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star pos d13 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:185 283043 | Sample 0256 081 FR NSP TR2 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_081_FR_NSP_TR2_SL1_S12_L001_R1_001-pooled.fastq.gz 0256_081_FR_NSP_TR2_SL1_S12_L001_R2_001-pooled.fastq.gz | fastq fastq | 2976324300.0 | 29179650.0 | ena RUN TAB 09 11 2022 11:52:59:185 283044 | 0:51 1:51 | A:831817738;C:637392987;G:662609648;T:844470228;N:33699 | 51 | 51 | 831817738 | 637392987 | 662609648 | 844470228 | 33699 | ERX9997155 | ERS13672480 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11094 | 11094 | ERR10476831 | ERX9997174 | ERS13672499 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day6 | SAMEA111562643 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d6 5|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star neg d6 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:193 283081 | Sample 0256 105 FR NSP TR1 SL2 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_105_FR_NSP_TR1_SL2_S34_L001_R1_001-pooled.fastq.gz 0256_105_FR_NSP_TR1_SL2_S34_L001_R2_001-pooled.fastq.gz | fastq fastq | 3118607160.0 | 30574580.0 | ena RUN TAB 09 11 2022 11:52:59:193 283082 | 0:51 1:51 | A:849321742;C:701271960;G:711995793;T:855982293;N:35372 | 51 | 51 | 849321742 | 701271960 | 711995793 | 855982293 | 35372 | ERX9997174 | ERS13672499 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11095 | 11095 | ERR10476793 | ERX9997136 | ERS13672461 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day13 | SAMEA111562605 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d13 2|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:tu wt d13 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:177 283005 | Sample 0256 007 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_007_FR_NSP_TR1_SL1_S19_L001_R1_001-pooled.fastq.gz 0256_007_FR_NSP_TR1_SL1_S19_L001_R2_001-pooled.fastq.gz | fastq fastq | 2806322430.0 | 27512965.0 | ena RUN TAB 09 11 2022 11:52:59:177 283006 | 0:51 1:51 | A:715863946;C:680964497;G:693755104;T:715642850;N:96033 | 51 | 51 | 715863946 | 680964497 | 693755104 | 715642850 | 96033 | ERX9997136 | ERS13672461 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11101 | 11101 | ERR10476795 | ERX9997138 | ERS13672463 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day13 | SAMEA111562607 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d13 4|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:tu wt d13 4|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:178 283009 | Sample 0256 009 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_009_FR_NSP_TR1_SL1_S20_L001_R1_001-pooled.fastq.gz 0256_009_FR_NSP_TR1_SL1_S20_L001_R2_001-pooled.fastq.gz | fastq fastq | 2524225518.0 | 24747309.0 | ena RUN TAB 09 11 2022 11:52:59:178 283010 | 0:51 1:51 | A:643453173;C:607310608;G:630496995;T:642879275;N:85467 | 51 | 51 | 643453173 | 607310608 | 630496995 | 642879275 | 85467 | ERX9997138 | ERS13672463 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11102 | 11102 | ERR10476792 | ERX9997135 | ERS13672460 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | wildtype whole brain pooled 15 brains | wildtype whole brain day13 | SAMEA111562604 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d13 1|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:tu wt d13 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:177 283003 | Sample 0256 006 FR NSP TR1 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_006_FR_NSP_TR1_SL1_S18_L001_R1_001-pooled.fastq.gz 0256_006_FR_NSP_TR1_SL1_S18_L001_R2_001-pooled.fastq.gz | fastq fastq | 2436931062.0 | 23891481.0 | ena RUN TAB 09 11 2022 11:52:59:177 283004 | 0:51 1:51 | A:622664838;C:583373590;G:613974641;T:616835192;N:82801 | 51 | 51 | 622664838 | 583373590 | 613974641 | 616835192 | 82801 | ERX9997135 | ERS13672460 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11104 | 11104 | ERR10476834 | ERX9997177 | ERS13672502 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC / whole brain pooled 15 brains | star:bPAC / whole brain day13 | SAMEA111562646 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d13 3|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star neg d13 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:195 283087 | Sample 0256 108 FR NSP TR2 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_108_FR_NSP_TR2_SL1_S37_L001_R1_001-pooled.fastq.gz 0256_108_FR_NSP_TR2_SL1_S37_L001_R2_001-pooled.fastq.gz | fastq fastq | 3252093438.0 | 31883269.0 | ena RUN TAB 09 11 2022 11:52:59:195 283088 | 0:51 1:51 | A:901696576;C:701023909;G:729587564;T:919748293;N:37096 | 51 | 51 | 901696576 | 701023909 | 729587564 | 919748293 | 37096 | ERX9997177 | ERS13672502 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11105 | 11105 | ERR10476815 | ERX9997158 | ERS13672483 | ERP138527 | PRJEB53713 | Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish | f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e | Other | Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | star:bPAC+/ whole brain pooled 15 brains | star:bPAC+/ whole brain day13 | SAMEA111562627 | Living Systems Institute, University of Exeter | INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d13 4|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star pos d13 4|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 09 11 2022 11:52:59:186 283049 | Sample 0256 084 FR NSP TR2 SL1 | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP138527 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 | 0256_084_FR_NSP_TR2_SL1_S15_L001_R1_001-pooled.fastq.gz 0256_084_FR_NSP_TR2_SL1_S15_L001_R2_001-pooled.fastq.gz | fastq fastq | 4118541720.0 | 40377860.0 | ena RUN TAB 09 11 2022 11:52:59:187 283050 | 0:51 1:51 | A:1136484689;C:909656648;G:924700451;T:1147653128;N:46804 | 51 | 51 | 1136484689 | 909656648 | 924700451 | 1147653128 | 46804 | ERX9997158 | ERS13672483 | ERA18581410 | living systems institute, university of exeter|European Nucleotide Archive | living systems institute, university of exeter|European Nucleotide Archive | B | B | biological fallback assumption | illumina | novaseq_era | full_length | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2024-02-06 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 11153 | 11153 | ERR10034052 | ERX9574456 | ERS12562167 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Larval tissue without xxx from Danio rerio | Drerio larval 5 | SAMEA110464139 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464139|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE5|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE5|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:829 19138 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr5.1.fastq.gz S879Nr5.2.fastq.gz | fastq fastq | 7308445864.0 | 36509997.0 | ena RUN TAB 05 08 2022 14:25:08:829 19139 | 0:100.09 1:100.09 | A:1934019972;C:1742739870;G:1803466955;T:1828120200;N:98867 | 100 | 100 | 1934019972 | 1742739870 | 1803466955 | 1828120200 | 98867 | ERX9574456 | ERS12562167 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.96596 | 0.96653 | 0.05312 | 0.05284 | 0.71323 | 0.71873 | 0.49632 | 0.48138 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Larval | Larval | Trunk | Surface Structure | ||||||||||||||
| 11154 | 11154 | ERR10034051 | ERX9574455 | ERS12562166 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Larval tissue without xxx from Danio rerio | Drerio larval 4 | SAMEA110464138 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464138|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE4|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE4|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:822 19136 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr4.1.fastq.gz S879Nr4.2.fastq.gz | fastq fastq | 8046902370.0 | 40206331.0 | ena RUN TAB 05 08 2022 14:25:08:829 19137 | 0:100.07 1:100.07 | A:2154247315;C:1901540683;G:1965167700;T:2025838764;N:107908 | 100 | 100 | 2154247315 | 1901540683 | 1965167700 | 2025838764 | 107908 | ERX9574455 | ERS12562166 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.96507 | 0.96543 | 0.05345 | 0.0533 | 0.71553 | 0.72123 | 0.48553 | 0.49 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Larval | Larval | Trunk | Surface Structure | ||||||||||||||
| 11155 | 11155 | ERR10034050 | ERX9574454 | ERS12562165 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Larval tissue without xxx from Danio rerio | Drerio larval 3 | SAMEA110464137 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464137|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE3|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE3|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:821 19134 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr3.1.fastq.gz S879Nr3.2.fastq.gz | fastq fastq | 10897526786.0 | 54442757.0 | ena RUN TAB 05 08 2022 14:25:08:821 19135 | 0:100.08 1:100.08 | A:2902340346;C:2590905706;G:2655361716;T:2748771201;N:147817 | 100 | 100 | 2902340346 | 2590905706 | 2655361716 | 2748771201 | 147817 | ERX9574454 | ERS12562165 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.93244 | 0.93322 | 0.04311 | 0.04269 | 0.72452 | 0.72723 | 0.49726 | 0.4784 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Larval | Larval | Trunk | Surface Structure | ||||||||||||||
| 11156 | 11156 | ERR10034049 | ERX9574453 | ERS12562164 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Larval tissue without xxx from Danio rerio | Drerio larval 2 | SAMEA110464136 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464136|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE2|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE2|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:821 19132 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr2.1.fastq.gz S879Nr2.2.fastq.gz | fastq fastq | 8516273680.0 | 42589650.0 | ena RUN TAB 05 08 2022 14:25:08:821 19133 | 0:99.98 1:99.98 | A:2232300748;C:2055212367;G:2121115843;T:2107529926;N:114796 | 99 | 99 | 2232300748 | 2055212367 | 2121115843 | 2107529926 | 114796 | ERX9574453 | ERS12562164 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.97117 | 0.97187 | 0.05876 | 0.05804 | 0.72115 | 0.72689 | 0.51447 | 0.50827 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Larval | Larval | Trunk | Surface Structure | ||||||||||||||
| 11157 | 11157 | ERR10034048 | ERX9574452 | ERS12562163 | ERP140005 | PRJEB55122 | Danio developmental transcriptomes | ca4a518e-aaf7-42d9-9758-352aac808809 | Other | Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. | ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08 | Larval tissue without xxx from Danio rerio | Drerio larval 1 | SAMEA110464135 | max planck institute for biology | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464135|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE1|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE1|sex:not provided|tissue type:whole body without xxx | Illumina NovaSeq 6000 paired end sequencing | ena EXPERIMENT TAB 05 08 2022 14:25:08:820 19130 | unspecified | 1 | Illumina TruSeq DNA Nano Kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP140005 | Illumina NovaSeq 6000 paired end sequencing | ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 | S879Nr1.1.fastq.gz S879Nr1.2.fastq.gz | fastq fastq | 5477863098.0 | 27332001.0 | ena RUN TAB 05 08 2022 14:25:08:821 19131 | 0:100.21 1:100.21 | A:1436230762;C:1320194529;G:1370010454;T:1351352868;N:74485 | 100 | 100 | 1436230762 | 1320194529 | 1370010454 | 1351352868 | 74485 | ERX9574452 | ERS12562163 | ERA16814395 | max planck institute for biology|European Nucleotide Archive | max planck institute for biology | 2 | 0.97196 | 0.97163 | 0.05932 | 0.05814 | 0.72723 | 0.73348 | 0.50582 | 0.51053 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2022-08-05 | Larval | Larval | Trunk | Surface Structure | ||||||||||||||
| 25316 | 25316 | SRR25786849 | SRX21509238 | SRS18740266 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | RNA seq Erythrocytes miR 144 mutant Danio rerio 3 dpf | CD KD 144 | strain:mir 144 mutant|age:3 days|collection date:not provided|geo loc name:not provided|sex:mixed|tissue:whole embryo|BioSampleModel:Model organism or animal | RNA seq Erythrocytes miR 144 mutant Danio rerio 3 dpf replicate 2 | CD KD 1442 | CD KD 1442 | Libraries were made using Illumina mRNA seq library prep kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_KD_1442-R_S4_L001_R2_001.fastq.gz CD_KD_1442-R_S4_L001_R1_001.fastq.gz | fastq fastq | 15176751228.0 | 77119924.0 | CD KD 1442 R S4 L001 R1 001.fastq.gz | 0:98.43 1:98.37 | A:3779746373;C:3784109407;G:3856858311;T:3696705097;N:59332040 | 98 | 98 | 3779746373 | 3784109407 | 3856858311 | 3696705097 | 59332040 | SRX21509238 | SRS18740266 | SRA1701488 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.97046 | 0.97577 | 0.04054 | 0.04056 | 0.84404 | 0.84368 | 0.44473 | 0.44497 | 99 | 100 | B | B | biological fallback assumption | illumina | nextseq_v2 | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2023-08-30 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||
| 25317 | 25317 | SRR25786850 | SRX21509237 | SRS18740266 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | RNA seq Erythrocytes miR 144 mutant Danio rerio 3 dpf | CD KD 144 | strain:mir 144 mutant|age:3 days|collection date:not provided|geo loc name:not provided|sex:mixed|tissue:whole embryo|BioSampleModel:Model organism or animal | RNA seq Erythrocytes miR 144 mutant Danio rerio 3 dpf replicate 1 | CD KD 1441 | CD KD 1441 | Libraries were made using Illumina mRNA seq library prep kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_KD_1441-R_S3_L001_R2_001.fastq.gz CD_KD_1441-R_S3_L001_R1_001.fastq.gz | fastq fastq | 12981589931.0 | 66199400.0 | CD KD 1441 R S3 L001 R1 001.fastq.gz | 0:98.08 1:98.02 | A:3222063377;C:3237477192;G:3298955148;T:3151608365;N:71485849 | 98 | 98 | 3222063377 | 3237477192 | 3298955148 | 3151608365 | 71485849 | SRX21509237 | SRS18740266 | SRA1701488 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.97163 | 0.97711 | 0.03644 | 0.03649 | 0.8188 | 0.81889 | 0.44686 | 0.44149 | 100 | 101 | B | B | biological fallback assumption | illumina | nextseq_v2 | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2023-08-30 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||
| 25318 | 25318 | SRR25786851 | SRX21509236 | SRS18740265 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | RNA seq Erythrocytes Wild type Danio rerio 3 dpf | CD KD WT | strain:Wildtype|age:3 days|collection date:not provided|geo loc name:not provided|sex:mixed|tissue:whole embryo|BioSampleModel:Model organism or animal | RNA seq Erythrocytes Wild type Danio rerio 3 dpf replicate 2 | CD KD WT2 | CD KD WT2 | Libraries were made using Illumina mRNA seq library prep kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_KD_WT2-R_S2_L001_R1_001.fastq.gz CD_KD_WT2-R_S2_L001_R2_001.fastq.gz | fastq fastq | 13841850598.0 | 71086657.0 | CD KD WT2 R S2 L001 R1 001.fastq.gz | 0:97.39 1:97.33 | A:3429992533;C:3433873133;G:3489428993;T:3365505686;N:123050253 | 97 | 97 | 3429992533 | 3433873133 | 3489428993 | 3365505686 | 123050253 | SRX21509236 | SRS18740265 | SRA1701488 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.97088 | 0.97596 | 0.03787 | 0.0381 | 0.84896 | 0.8496 | 0.45727 | 0.45346 | 101 | 101 | B | B | biological fallback assumption | illumina | nextseq_v2 | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2023-08-30 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||
| 25319 | 25319 | SRR25786852 | SRX21509235 | SRS18740265 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | RNA seq Erythrocytes Wild type Danio rerio 3 dpf | CD KD WT | strain:Wildtype|age:3 days|collection date:not provided|geo loc name:not provided|sex:mixed|tissue:whole embryo|BioSampleModel:Model organism or animal | RNA seq Erythrocytes Wild type Danio rerio 3 dpf replicate 1 | CD KD WT1 | CD KD WT1 | Libraries were made using Illumina mRNA seq library prep kit | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_KD_WT1-R_S1_L001_R1_001.fastq.gz CD_KD_WT1-R_S1_L001_R2_001.fastq.gz | fastq fastq | 13279321095.0 | 67105432.0 | CD KD WT1 R S1 L001 R1 001.fastq.gz | 0:98.98 1:98.91 | A:3310018513;C:3313506420;G:3374819099;T:3243710775;N:37266288 | 98 | 98 | 3310018513 | 3313506420 | 3374819099 | 3243710775 | 37266288 | SRX21509235 | SRS18740265 | SRA1701488 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.97038 | 0.97604 | 0.04235 | 0.04238 | 0.83676 | 0.8367 | 0.45607 | 0.45443 | 101 | 101 | B | B | biological fallback assumption | illumina | nextseq_v2 | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2023-08-30 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||
| 29259 | 29259 | SRR27336917 | SRX23013778 | SRS19977075 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalKO gonads 31dpf rep2 | miR214 PaternalKO gonads 31dpf rep2 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A11 | miR214 PaternalKO gonads 31dpf rep2 | miR214 PaternalKO gonads 31dpf rep2 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalKO_gonads_31dpf_rep2.fastq.gz | fastq | 2327996832.0 | 27714248.0 | miR214 PaternalKO gonads 31dpf rep2.fastq.gz | 0:84 | A:602135965;C:552786494;G:537368428;T:635697339;N:8606 | 84 | 602135965 | 552786494 | 537368428 | 635697339 | 8606 | SRX23013778 | SRS19977075 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95369 | 0.06146 | 0.69203 | 0.47259 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29260 | 29260 | SRR27336918 | SRX23013777 | SRS19977074 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalKO gonads 31dpf rep1 | miR214 PaternalKO gonads 31dpf rep1 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A10 | miR214 PaternalKO gonads 31dpf rep1 | miR214 PaternalKO gonads 31dpf rep1 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalKO_gonads_31dpf_rep1.fastq.gz | fastq | 2500978452.0 | 29773553.0 | miR214 PaternalKO gonads 31dpf rep1.fastq.gz | 0:84 | A:646162933;C:593855971;G:578265372;T:682684551;N:9625 | 84 | 646162933 | 593855971 | 578265372 | 682684551 | 9625 | SRX23013777 | SRS19977074 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95147 | 0.05972 | 0.69071 | 0.47043 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29261 | 29261 | SRR27336919 | SRX23013776 | SRS19977073 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 maternalHET gonads 31dpf rep4 | miR214 maternalHET gonads 31dpf rep4 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep4|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A9 | miR214 maternalHET gonads 31dpf rep4 | miR214 maternalHET gonads 31dpf rep4 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_maternalHET_gonads_31dpf_rep4.fastq.gz | fastq | 2365480908.0 | 28160487.0 | miR214 maternalHET gonads 31dpf rep4.fastq.gz | 0:84 | A:613121312;C:560582165;G:549338096;T:642429834;N:9501 | 84 | 613121312 | 560582165 | 549338096 | 642429834 | 9501 | SRX23013776 | SRS19977073 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95304 | 0.05342 | 0.7108 | 0.46822 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29262 | 29262 | SRR27336920 | SRX23013775 | SRS19977072 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 maternalHET gonads 31dpf rep3 | miR214 maternalHET gonads 31dpf rep3 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep3|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A8 | miR214 maternalHET gonads 31dpf rep3 | miR214 maternalHET gonads 31dpf rep3 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_maternalHET_gonads_31dpf_rep3.fastq.gz | fastq | 2537794644.0 | 30211841.0 | miR214 maternalHET gonads 31dpf rep3.fastq.gz | 0:84 | A:658687178;C:600742464;G:585643169;T:692712057;N:9776 | 84 | 658687178 | 600742464 | 585643169 | 692712057 | 9776 | SRX23013775 | SRS19977072 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95177 | 0.06701 | 0.68195 | 0.47393 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29263 | 29263 | SRR27336921 | SRX23013774 | SRS19977071 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 maternalHET gonads 31dpf rep2 | miR214 maternalHET gonads 31dpf rep2 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep2|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A7 | miR214 maternalHET gonads 31dpf rep2 | miR214 maternalHET gonads 31dpf rep2 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_maternalHET_gonads_31dpf_rep2.fastq.gz | fastq | 2417384424.0 | 28778386.0 | miR214 maternalHET gonads 31dpf rep2.fastq.gz | 0:84 | A:625935186;C:574179061;G:560498085;T:656762980;N:9112 | 84 | 625935186 | 574179061 | 560498085 | 656762980 | 9112 | SRX23013774 | SRS19977071 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95259 | 0.05852 | 0.6981 | 0.47435 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29264 | 29264 | SRR27336922 | SRX23013773 | SRS19977070 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 maternalHET gonads 31dpf rep1 | miR214 maternalHET gonads 31dpf rep1 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep1|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A6 | miR214 maternalHET gonads 31dpf rep1 | miR214 maternalHET gonads 31dpf rep1 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_maternalHET_gonads_31dpf_rep1.fastq.gz | fastq | 2330886180.0 | 27748645.0 | miR214 maternalHET gonads 31dpf rep1.fastq.gz | 0:84 | A:601589571;C:554105326;G:542789267;T:632393158;N:8858 | 84 | 601589571 | 554105326 | 542789267 | 632393158 | 8858 | SRX23013773 | SRS19977070 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95338 | 0.05239 | 0.71366 | 0.47291 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29265 | 29265 | SRR27336923 | SRX23013772 | SRS19977069 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 maternalKO gonads 31dpf rep4 | miR214 maternalKO gonads 31dpf rep4 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A5 | miR214 maternalKO gonads 31dpf rep4 | miR214 maternalKO gonads 31dpf rep4 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_maternalKO_gonads_31dpf_rep4.fastq.gz | fastq | 2340233784.0 | 27859926.0 | miR214 maternalKO gonads 31dpf rep4.fastq.gz | 0:84 | A:606735187;C:553647808;G:539865459;T:639976430;N:8900 | 84 | 606735187 | 553647808 | 539865459 | 639976430 | 8900 | SRX23013772 | SRS19977069 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95406 | 0.06415 | 0.68225 | 0.47695 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29266 | 29266 | SRR27336924 | SRX23013771 | SRS19977068 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 maternalKO gonads 31dpf rep3 | miR214 maternalKO gonads 31dpf rep3 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A4 | miR214 maternalKO gonads 31dpf rep3 | miR214 maternalKO gonads 31dpf rep3 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_maternalKO_gonads_31dpf_rep3.fastq.gz | fastq | 2058505512.0 | 24506018.0 | miR214 maternalKO gonads 31dpf rep3.fastq.gz | 0:84 | A:537425814;C:485664494;G:471526682;T:563881213;N:7309 | 84 | 537425814 | 485664494 | 471526682 | 563881213 | 7309 | SRX23013771 | SRS19977068 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95296 | 0.06728 | 0.69266 | 0.47627 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29267 | 29267 | SRR27336925 | SRX23013770 | SRS19977067 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalHET gonads 31dpf rep4 | miR214 PaternalHET gonads 31dpf rep4 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep4|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A17 | miR214 PaternalHET gonads 31dpf rep4 | miR214 PaternalHET gonads 31dpf rep4 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalHET_gonads_31dpf_rep4.fastq.gz | fastq | 3001613328.0 | 35733492.0 | miR214 PaternalHET gonads 31dpf rep4.fastq.gz | 0:84 | A:778860501;C:711155422;G:688784969;T:822801157;N:11279 | 84 | 778860501 | 711155422 | 688784969 | 822801157 | 11279 | SRX23013770 | SRS19977067 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95361 | 0.05653 | 0.7051 | 0.48382 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29268 | 29268 | SRR27336926 | SRX23013769 | SRS19977066 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalHET gonads 31dpf rep3 | miR214 PaternalHET gonads 31dpf rep3 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A16 | miR214 PaternalHET gonads 31dpf rep3 | miR214 PaternalHET gonads 31dpf rep3 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalHET_gonads_31dpf_rep3.fastq.gz | fastq | 3053630664.0 | 36352746.0 | miR214 PaternalHET gonads 31dpf rep3.fastq.gz | 0:84 | A:785219727;C:726431662;G:713454025;T:828513556;N:11694 | 84 | 785219727 | 726431662 | 713454025 | 828513556 | 11694 | SRX23013769 | SRS19977066 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95309 | 0.04588 | 0.71997 | 0.46447 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29269 | 29269 | SRR27336927 | SRX23013768 | SRS19977065 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalHET gonads 31dpf rep2 | miR214 PaternalHET gonads 31dpf rep2 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A15 | miR214 PaternalHET gonads 31dpf rep2 | miR214 PaternalHET gonads 31dpf rep2 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalHET_gonads_31dpf_rep2.fastq.gz | fastq | 3063695208.0 | 36472562.0 | miR214 PaternalHET gonads 31dpf rep2.fastq.gz | 0:84 | A:784924646;C:728941687;G:720847462;T:828969510;N:11903 | 84 | 784924646 | 728941687 | 720847462 | 828969510 | 11903 | SRX23013768 | SRS19977065 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95413 | 0.04739 | 0.71936 | 0.4704 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29270 | 29270 | SRR27336928 | SRX23013767 | SRS19977064 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalHET gonads 31dpf rep1 | miR214 PaternalHET gonads 31dpf rep1 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A14 | miR214 PaternalHET gonads 31dpf rep1 | miR214 PaternalHET gonads 31dpf rep1 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalHET_gonads_31dpf_rep1.fastq.gz | fastq | 2699154024.0 | 32132786.0 | miR214 PaternalHET gonads 31dpf rep1.fastq.gz | 0:84 | A:694174797;C:642049572;G:627991562;T:734927762;N:10331 | 84 | 694174797 | 642049572 | 627991562 | 734927762 | 10331 | SRX23013767 | SRS19977064 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95518 | 0.05525 | 0.70285 | 0.47695 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29271 | 29271 | SRR27336929 | SRX23013766 | SRS19977063 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalKO gonads 31dpf rep4 | miR214 PaternalKO gonads 31dpf rep4 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A13 | miR214 PaternalKO gonads 31dpf rep4 | miR214 PaternalKO gonads 31dpf rep4 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalKO_gonads_31dpf_rep4.fastq.gz | fastq | 2514248016.0 | 29931524.0 | miR214 PaternalKO gonads 31dpf rep4.fastq.gz | 0:84 | A:648908956;C:598837726;G:580002743;T:686488678;N:9913 | 84 | 648908956 | 598837726 | 580002743 | 686488678 | 9913 | SRX23013766 | SRS19977063 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.94978 | 0.06951 | 0.67896 | 0.47686 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29272 | 29272 | SRR27336930 | SRX23013765 | SRS19977062 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalKO gonads 31dpf rep3 | miR214 PaternalKO gonads 31dpf rep3 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A12 | miR214 PaternalKO gonads 31dpf rep3 | miR214 PaternalKO gonads 31dpf rep3 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalKO_gonads_31dpf_rep3.fastq.gz | fastq | 2499529200.0 | 29756300.0 | miR214 PaternalKO gonads 31dpf rep3.fastq.gz | 0:84 | A:642490769;C:597403823;G:580565141;T:679060154;N:9313 | 84 | 642490769 | 597403823 | 580565141 | 679060154 | 9313 | SRX23013765 | SRS19977062 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95284 | 0.05602 | 0.70289 | 0.47154 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29273 | 29273 | SRR27336931 | SRX23013764 | SRS19977061 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 maternalKO gonads 31dpf rep2 | miR214 maternalKO gonads 31dpf rep2 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A3 | miR214 maternalKO gonads 31dpf rep2 | miR214 maternalKO gonads 31dpf rep2 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_maternalKO_gonads_31dpf_rep2.fastq.gz | fastq | 2529742404.0 | 30115981.0 | miR214 maternalKO gonads 31dpf rep2.fastq.gz | 0:84 | A:652091166;C:600932059;G:589100617;T:687608862;N:9700 | 84 | 652091166 | 600932059 | 589100617 | 687608862 | 9700 | SRX23013764 | SRS19977061 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95498 | 0.05524 | 0.70366 | 0.47319 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 29274 | 29274 | SRR27336932 | SRX23013763 | SRS19977060 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 maternalKO gonads 31dpf rep1 | miR214 maternalKO gonads 31dpf rep1 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A2 | miR214 maternalKO gonads 31dpf rep1 | miR214 maternalKO gonads 31dpf rep1 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_maternalKO_gonads_31dpf_rep1.fastq.gz | fastq | 2310878136.0 | 27510454.0 | miR214 maternalKO gonads 31dpf rep1.fastq.gz | 0:84 | A:598541924;C:547875391;G:533137786;T:631314274;N:8761 | 84 | 598541924 | 547875391 | 533137786 | 631314274 | 8761 | SRX23013763 | SRS19977060 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95279 | 0.06446 | 0.68757 | 0.4758 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System | ||||||||||||||||||||||||||
| 30605 | 30605 | SRR27885298 | SRX23547062 | SRS20394839 | SRP488393 | PRJNA1073712 | Danio rerio Raw sequence reads | PRJNA1073712 | Whole Genome Sequencing | normal RNAseq of Danio rerio | Treat3 | breed:AB|dev stage:7 dpf|collection date:2022 01 06|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=treat biolobical replicate 3|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | t3 | t3 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP488393 | treat3_1.fq.gz treat3_2.fq.gz | fastq fastq | 11227897200.0 | 37426324.0 | treat3 1.fq.gz | 0:150 1:150 | A:2841991870;C:2760705502;G:2843113319;T:2781984816;N:101693 | 150 | 150 | 2841991870 | 2760705502 | 2843113319 | 2781984816 | 101693 | SRX23547062 | SRS20394839 | SRA1798310 | Wuhan University|School of Basic Medical Sciences | Wuhan University | 2 | 0.9395 | 0.93765 | 0.03042 | 0.02991 | 0.75943 | 0.76282 | 0.52931 | 0.52802 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-02-06 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||
| 30606 | 30606 | SRR27885299 | SRX23547061 | SRS20394838 | SRP488393 | PRJNA1073712 | Danio rerio Raw sequence reads | PRJNA1073712 | Whole Genome Sequencing | normal RNAseq of Danio rerio | Control3 | breed:AB|dev stage:7 dpf|collection date:2022 01 06|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=control biolobical replicate 3|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | c3 | c3 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP488393 | control3_1.fq.gz control3_2.fq.gz | fastq fastq | 13204860600.0 | 44016202.0 | control3 1.fq.gz | 0:150 1:150 | A:3362002161;C:3237033953;G:3340888463;T:3264815850;N:120173 | 150 | 150 | 3362002161 | 3237033953 | 3340888463 | 3264815850 | 120173 | SRX23547061 | SRS20394838 | SRA1798310 | Wuhan University|School of Basic Medical Sciences | Wuhan University | 2 | 0.94114 | 0.94099 | 0.03313 | 0.0336 | 0.7611 | 0.76562 | 0.52598 | 0.54255 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-02-06 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||
| 30607 | 30607 | SRR27885300 | SRX23547060 | SRS20394837 | SRP488393 | PRJNA1073712 | Danio rerio Raw sequence reads | PRJNA1073712 | Whole Genome Sequencing | normal RNAseq of Danio rerio | Treat2 | breed:AB|dev stage:7 dpf|collection date:2022 01 02|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=treat biolobical replicate 2|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | t2 | t2 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP488393 | treat2_1.fq.gz treat2_2.fq.gz | fastq fastq | 13686972300.0 | 45623241.0 | treat2 1.fq.gz | 0:150 1:150 | A:3497540140;C:3330959709;G:3473656510;T:3384780397;N:35544 | 150 | 150 | 3497540140 | 3330959709 | 3473656510 | 3384780397 | 35544 | SRX23547060 | SRS20394837 | SRA1798310 | Wuhan University|School of Basic Medical Sciences | Wuhan University | 2 | 0.94978 | 0.9476 | 0.02247 | 0.02209 | 0.77508 | 0.78104 | 0.5376 | 0.54975 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-02-06 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||
| 30608 | 30608 | SRR27885301 | SRX23547059 | SRS20394836 | SRP488393 | PRJNA1073712 | Danio rerio Raw sequence reads | PRJNA1073712 | Whole Genome Sequencing | normal RNAseq of Danio rerio | Control2 | breed:AB|dev stage:7 dpf|collection date:2022 01 02|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=control biolobical replicate 2|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | c2 | c2 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP488393 | control2_1.fq.gz control2_2.fq.gz | fastq fastq | 13075274400.0 | 43584248.0 | control2 1.fq.gz | 0:150 1:150 | A:3297304643;C:3196925316;G:3364735785;T:3216273784;N:34872 | 150 | 150 | 3297304643 | 3196925316 | 3364735785 | 3216273784 | 34872 | SRX23547059 | SRS20394836 | SRA1798310 | Wuhan University|School of Basic Medical Sciences | Wuhan University | 2 | 0.94539 | 0.94301 | 0.02162 | 0.02151 | 0.78358 | 0.78886 | 0.53728 | 0.52362 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-02-06 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||
| 30609 | 30609 | SRR27885302 | SRX23547058 | SRS20394835 | SRP488393 | PRJNA1073712 | Danio rerio Raw sequence reads | PRJNA1073712 | Whole Genome Sequencing | normal RNAseq of Danio rerio | Treat1 | breed:AB|dev stage:7 dpf|collection date:2021 12 22|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=treat biolobical replicate 1|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | t1 | t1 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP488393 | treat1_1.fq.gz treat1_2.fq.gz | fastq fastq | 14810228700.0 | 49367429.0 | treat1 1.fq.gz | 0:150 1:150 | A:3737682638;C:3643663419;G:3815975423;T:3612867530;N:39690 | 150 | 150 | 3737682638 | 3643663419 | 3815975423 | 3612867530 | 39690 | SRX23547058 | SRS20394835 | SRA1798310 | Wuhan University|School of Basic Medical Sciences | Wuhan University | 2 | 0.94911 | 0.94637 | 0.0196 | 0.0194 | 0.76928 | 0.77406 | 0.52665 | 0.53607 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-02-06 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||
| 30610 | 30610 | SRR27885303 | SRX23547057 | SRS20394834 | SRP488393 | PRJNA1073712 | Danio rerio Raw sequence reads | PRJNA1073712 | Whole Genome Sequencing | normal RNAseq of Danio rerio | Control1 | breed:AB|dev stage:7 dpf|collection date:2021 12 22|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=control biolobical replicate 1|BioSampleModel:Model organism or animal | RNA seq of Danio rerio | c1 | c1 | normal RNA seq of Danio rerio | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP488393 | control1_1.fq.gz control1_2.fq.gz | fastq fastq | 13024707900.0 | 43415693.0 | control1 1.fq.gz | 0:150 1:150 | A:3266649802;C:3212798200;G:3383472165;T:3161753039;N:34694 | 150 | 150 | 3266649802 | 3212798200 | 3383472165 | 3161753039 | 34694 | SRX23547057 | SRS20394834 | SRA1798310 | Wuhan University|School of Basic Medical Sciences | Wuhan University | 2 | 0.93586 | 0.9333 | 0.02078 | 0.02096 | 0.77197 | 0.77729 | 0.53822 | 0.52512 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-02-06 | Larval | Larval | Liver | Liver and Biliary 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");;