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26 rows where experiment.library_selection = "other", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Multi-tissue"

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 26 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 26 ✖

experiment.library_source 1

experiment.library_selection 1

  • other · 26 ✖

experiment.library_layout 1

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
10206 10206 ERR6474244 ERX6101519 ERS7377049 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… InputFISH E MTAB 10834:InputFISH   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:InputFISH p InputFISH p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:input DNA|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 InputFISH.R1.fastq.gz InputFISH.R2.fastq.gz fastq fastq 2014534500.0 24271500.0 E MTAB 10834:InputFISH.R 0:40 1:43 A:435725523;C:539145149;G:601092466;T:438298953;N:272409 40 43     435725523 539145149 601092466 438298953 272409 ERX6101519 ERS7377049 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.394 0.34957 0.09053 0.09378 0.96485 0.97323 0.73467 0.62676 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10207 10207 ERR6474223 ERX6101498 ERS7377028 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… hsHuRFISH rep2 E MTAB 10834:hsHuRFISH rep2   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:hsHuRFISH rep2 p hsHuRFISH rep2 p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti hsHuR|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 hsHuRFISH_rep2.R2.fastq.gz hsHuRFISH_rep2.R1.fastq.gz fastq fastq 2106598100.0 25380700.0 E MTAB 10834:hsHuRFISH rep2.R 0:40 1:43 A:503141361;C:548220448;G:569927989;T:485014455;N:293847 40 43     503141361 548220448 569927989 485014455 293847 ERX6101498 ERS7377028 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.76055 0.70626 0.18785 0.18742 0.92387 0.93533 0.72831 0.65481 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10208 10208 ERR6474222 ERX6101497 ERS7377027 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… hsHuRFISH rep1 E MTAB 10834:hsHuRFISH rep1   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:hsHuRFISH rep1 p hsHuRFISH rep1 p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti hsHuR|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 hsHuRFISH_rep1.R1.fastq.gz hsHuRFISH_rep1.R2.fastq.gz fastq fastq 2520623431.0 30368957.0 E MTAB 10834:hsHuRFISH rep1.R 0:40 1:43 A:604086659;C:653262791;G:679919989;T:582992802;N:361190 40 43     604086659 653262791 679919989 582992802 361190 ERX6101497 ERS7377027 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.76096 0.70783 0.18844 0.18848 0.92101 0.93275 0.7333 0.62616 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10209 10209 ERR6474221 ERX6101496 ERS7377026 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… HaloFISH E MTAB 10834:HaloFISH   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:HaloFISH p HaloFISH p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti HaloTag|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 HaloFISH.R2.fastq.gz HaloFISH.R1.fastq.gz fastq fastq 2353027590.0 28349730.0 E MTAB 10834:HaloFISH.R 0:40 1:43 A:522964401;C:650152942;G:677020220;T:502555313;N:334714 40 43     522964401 650152942 677020220 502555313 334714 ERX6101496 ERS7377026 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.82307 0.78117 0.18309 0.18609 0.93888 0.94627 0.73861 0.63812 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10210 10210 ERR6474216 ERX6101492 ERS7377022 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… drHuRFISH rep2 E MTAB 10834:drHuRFISH rep2   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:drHuRFISH rep2 p drHuRFISH rep2 p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti drHuR|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 drHuRFISH_rep2.R1.fastq.gz drHuRFISH_rep2.R2.fastq.gz fastq fastq 2408024386.0 29012342.0 E MTAB 10834:drHuRFISH rep2.R 0:40 1:43 A:566287649;C:627743498;G:663052609;T:550604982;N:335648 40 43     566287649 627743498 663052609 550604982 335648 ERX6101492 ERS7377022 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.68524 0.62721 0.16916 0.1656 0.93501 0.94541 0.7028 0.64738 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10211 10211 ERR6474215 ERX6101491 ERS7377021 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… drHuRFISH rep1 E MTAB 10834:drHuRFISH rep1   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:drHuRFISH rep1 p drHuRFISH rep1 p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti drHuR|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 drHuRFISH_rep1.R1.fastq.gz drHuRFISH_rep1.R2.fastq.gz fastq fastq 3025188980.0 36448060.0 E MTAB 10834:drHuRFISH rep1.R 0:40 1:43 A:720153781;C:784188971;G:824077525;T:696330222;N:438481 40 43     720153781 784188971 824077525 696330222 438481 ERX6101491 ERS7377021 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.7001 0.64217 0.17626 0.1728 0.93154 0.94249 0.72494 0.65821 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10342 10342 ERR7720665 ERX7289629 ERS9293395 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Nevi 3 SAMEA11646688 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646688|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Nevi 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 3|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Nevi 3 p Nevi 3 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Nevi-3_1.fastq.gz Nevi-3_2.fastq.gz fastq fastq 8483600160.0 53022501.0 E MTAB 7464 2:Nevi 3 0:80 1:80 A:2299114269;C:1922614492;G:1990271122;T:2270860686;N:739591 80 80     2299114269 1922614492 1990271122 2270860686 739591 ERX7289629 ERS9293395 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93346 0.93983 0.10878 0.10282 0.72608 0.72368 0.45081 0.44901 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10343 10343 ERR7720664 ERX7289628 ERS9293394 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Nevi 2 SAMEA11646687 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646687|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Nevi 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 2|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Nevi 2 p Nevi 2 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Nevi-2_1.fastq.gz Nevi-2_2.fastq.gz fastq fastq 9002687680.0 56266798.0 E MTAB 7464 2:Nevi 2 0:80 1:80 A:2446965759;C:2045918133;G:2107744175;T:2400665463;N:1394150 80 80     2446965759 2045918133 2107744175 2400665463 1394150 ERX7289628 ERS9293394 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93879 0.94198 0.1057 0.10023 0.7289 0.72874 0.45656 0.45677 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10344 10344 ERR7720663 ERX7289627 ERS9293393 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Nevi 1 SAMEA11646686 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646686|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Nevi 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 1|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Nevi 1 p Nevi 1 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Nevi-1_1.fastq.gz Nevi-1_2.fastq.gz fastq fastq 9332077600.0 58325485.0 E MTAB 7464 2:Nevi 1 0:80 1:80 A:2559136296;C:2096458598;G:2152359634;T:2522670596;N:1452476 80 80     2559136296 2096458598 2152359634 2522670596 1452476 ERX7289627 ERS9293393 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93341 0.93788 0.12721 0.12045 0.71181 0.71104 0.45834 0.46252 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10345 10345 ERR7720662 ERX7289626 ERS9293392 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Melanoma 4 SAMEA11646685 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646685|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Melanoma 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 4|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Melanoma 4 p Melanoma 4 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Melanoma-4_1.fastq.gz Melanoma-4_2.fastq.gz fastq fastq 8435873280.0 52724208.0 E MTAB 7464 2:Melanoma 4 0:80 1:80 A:2339229980;C:1858003608;G:1925352938;T:2311974102;N:1312652 80 80     2339229980 1858003608 1925352938 2311974102 1312652 ERX7289626 ERS9293392 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93101 0.93509 0.11646 0.10875 0.73647 0.73742 0.5229 0.52491 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10346 10346 ERR7720661 ERX7289625 ERS9293391 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Melanoma 3 SAMEA11646684 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646684|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Melanoma 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 3|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Melanoma 3 p Melanoma 3 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Melanoma-3_1.fastq.gz Melanoma-3_2.fastq.gz fastq fastq 8652678880.0 54079243.0 E MTAB 7464 2:Melanoma 3 0:80 1:80 A:2358154757;C:1941914032;G:2017842865;T:2333420807;N:1346419 80 80     2358154757 1941914032 2017842865 2333420807 1346419 ERX7289625 ERS9293391 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93095 0.93482 0.11494 0.10979 0.74878 0.74801 0.54149 0.54333 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10347 10347 ERR7720660 ERX7289624 ERS9293390 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Melanoma 2 SAMEA11646683 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646683|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Melanoma 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 2|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Melanoma 2 p Melanoma 2 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Melanoma-2_1.fastq.gz Melanoma-2_2.fastq.gz fastq fastq 9474565280.0 59216033.0 E MTAB 7464 2:Melanoma 2 0:80 1:80 A:2592490883;C:2143181332;G:2197827206;T:2539575741;N:1490118 80 80     2592490883 2143181332 2197827206 2539575741 1490118 ERX7289624 ERS9293390 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93925 0.94448 0.10906 0.10386 0.73768 0.73722 0.51879 0.51954 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10348 10348 ERR7720659 ERX7289623 ERS9293389 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Melanoma 1 SAMEA11646682 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646682|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Melanoma 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 1|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Melanoma 1 p Melanoma 1 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Melanoma-1_1.fastq.gz Melanoma-1_2.fastq.gz fastq fastq 8202724480.0 51267028.0 E MTAB 7464 2:Melanoma 1 0:80 1:80 A:2226523748;C:1862763739;G:1929197629;T:2182962113;N:1277251 80 80     2226523748 1862763739 1929197629 2182962113 1277251 ERX7289623 ERS9293389 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93514 0.9398 0.10447 0.09961 0.71697 0.71715 0.50157 0.50305 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10349 10349 ERR7720658 ERX7289622 ERS9293388 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Ctrl R 4 SAMEA11646681 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646681|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl R 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 4|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Ctrl R 4 p Ctrl R 4 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:n1|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Ctrl-R-4_1.fastq.gz Ctrl-R-4_2.fastq.gz fastq fastq 12134105440.0 75838159.0 E MTAB 7464 2:Ctrl R 4 0:80 1:80 A:3262023701;C:2677095735;G:2964643096;T:3227367048;N:2975860 80 80     3262023701 2677095735 2964643096 3227367048 2975860 ERX7289622 ERS9293388 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.91148 0.90942 0.31684 0.30692 0.7517 0.75708 0.51896 0.51898 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10350 10350 ERR7720657 ERX7289621 ERS9293387 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Ctrl R 3 SAMEA11646680 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646680|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl R 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 3|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Ctrl R 3 p Ctrl R 3 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:n1|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Ctrl-R-3_1.fastq.gz Ctrl-R-3_2.fastq.gz fastq fastq 10198941920.0 63743387.0 E MTAB 7464 2:Ctrl R 3 0:80 1:80 A:2707258482;C:2295053882;G:2521099885;T:2673029444;N:2500227 80 80     2707258482 2295053882 2521099885 2673029444 2500227 ERX7289621 ERS9293387 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.88031 0.87949 0.30603 0.30519 0.76219 0.76798 0.52516 0.51963 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10351 10351 ERR7720656 ERX7289620 ERS9293386 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Ctrl R 2 SAMEA11646679 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646679|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl R 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 2|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Ctrl R 2 p Ctrl R 2 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:n1|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Ctrl-R-2_1.fastq.gz Ctrl-R-2_2.fastq.gz fastq fastq 13001272960.0 81257956.0 E MTAB 7464 2:Ctrl R 2 0:80 1:80 A:3429977204;C:2902807573;G:3288394622;T:3376870832;N:3222729 80 80     3429977204 2902807573 3288394622 3376870832 3222729 ERX7289620 ERS9293386 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.89444 0.89377 0.30516 0.30529 0.75773 0.76769 0.52784 0.52192 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10352 10352 ERR7720655 ERX7289619 ERS9293385 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Ctrl R 1 SAMEA11646678 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646678|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl R 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 1|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Ctrl R 1 p Ctrl R 1 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:n1|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Ctrl-R-1_1.fastq.gz Ctrl-R-1_2.fastq.gz fastq fastq 10689399040.0 66808744.0 E MTAB 7464 2:Ctrl R 1 0:80 1:80 A:2897858681;C:2320332197;G:2613694217;T:2854881563;N:2632382 80 80     2897858681 2320332197 2613694217 2854881563 2632382 ERX7289619 ERS9293385 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.87124 0.87083 0.30804 0.30796 0.74596 0.75668 0.49784 0.50675 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10353 10353 ERR7720654 ERX7289618 ERS9293384 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Ctrl MN 3 SAMEA11646677 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646677|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl MN 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 3|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Ctrl MN 3 p Ctrl MN 3 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Ctrl-MN-3_1.fastq.gz Ctrl-MN-3_2.fastq.gz fastq fastq 7551734240.0 47198339.0 E MTAB 7464 2:Ctrl MN 3 0:80 1:80 A:2046757744;C:1713576176;G:1763123655;T:2027090307;N:1186358 80 80     2046757744 1713576176 1763123655 2027090307 1186358 ERX7289618 ERS9293384 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93513 0.93893 0.11198 0.10677 0.7232 0.72267 0.44068 0.4478 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10354 10354 ERR7720653 ERX7289617 ERS9293383 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Ctrl MN 2 SAMEA11646676 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646676|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl MN 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 2|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Ctrl MN 2 p Ctrl MN 2 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Ctrl-MN-2_1.fastq.gz Ctrl-MN-2_2.fastq.gz fastq fastq 8217322560.0 51358266.0 E MTAB 7464 2:Ctrl MN 2 0:80 1:80 A:2206636607;C:1895861057;G:1945883692;T:2167661877;N:1279327 80 80     2206636607 1895861057 1945883692 2167661877 1279327 ERX7289617 ERS9293383 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.94029 0.94525 0.10143 0.09713 0.72251 0.72036 0.44465 0.44591 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10355 10355 ERR7720652 ERX7289616 ERS9293382 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Ctrl MN 1 SAMEA11646675 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646675|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl MN 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 1|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:Ctrl MN 1 p Ctrl MN 1 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 Ctrl-MN-1_1.fastq.gz Ctrl-MN-1_2.fastq.gz fastq fastq 8135337280.0 50845858.0 E MTAB 7464 2:Ctrl MN 1 0:80 1:80 A:2202274973;C:1853973619;G:1910166269;T:2167658174;N:1264245 80 80     2202274973 1853973619 1910166269 2167658174 1264245 ERX7289616 ERS9293382 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.93729 0.94287 0.10448 0.09933 0.72585 0.72612 0.45373 0.45518 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10356 10356 ERR7720651 ERX7289615 ERS9293381 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 7dpa 3 SAMEA11646674 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646674|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:7dpa 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:7dpa 3|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:7dpa 3 p 7dpa 3 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 7dpa-3_1.fastq.gz 7dpa-3_2.fastq.gz fastq fastq 9873881440.0 61711759.0 E MTAB 7464 2:7dpa 3 0:80 1:80 A:2682240945;C:2177286149;G:2380282226;T:2631847017;N:2225103 80 80     2682240945 2177286149 2380282226 2631847017 2225103 ERX7289615 ERS9293381 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.83718 0.84277 0.3425 0.34639 0.73801 0.75035 0.51021 0.49835 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10357 10357 ERR7720650 ERX7289614 ERS9293380 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 7dpa 2 SAMEA11646673 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646673|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:7dpa 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:7dpa 2|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:7dpa 2 p 7dpa 2 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 7dpa-2_1.fastq.gz 7dpa-2_2.fastq.gz fastq fastq 12193073280.0 76206708.0 E MTAB 7464 2:7dpa 2 0:80 1:80 A:3333326821;C:2692186511;G:2887657057;T:3277111703;N:2791188 80 80     3333326821 2692186511 2887657057 3277111703 2791188 ERX7289614 ERS9293380 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.84944 0.85085 0.36391 0.36512 0.72496 0.73511 0.50367 0.49643 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10358 10358 ERR7720649 ERX7289613 ERS9293379 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 7dpa 1 SAMEA11646672 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646672|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:7dpa 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:7dpa 1|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:7dpa 1 p 7dpa 1 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 7dpa-1_1.fastq.gz 7dpa-1_2.fastq.gz fastq fastq 11533139040.0 72082119.0 E MTAB 7464 2:7dpa 1 0:80 1:80 A:3069170319;C:2575356466;G:2889466424;T:2996503729;N:2642102 80 80     3069170319 2575356466 2889466424 2996503729 2642102 ERX7289613 ERS9293379 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.86542 0.86857 0.33902 0.34263 0.7288 0.74186 0.50529 0.50071 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10359 10359 ERR7720648 ERX7289612 ERS9293378 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 1dpa 3 SAMEA11646671 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646671|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:1dpa 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:1dpa 3|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:1dpa 3 p 1dpa 3 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 1dpa-3_1.fastq.gz 1dpa-3_2.fastq.gz fastq fastq 13728291840.0 85801824.0 E MTAB 7464 2:1dpa 3 0:80 1:80 A:3747242594;C:3041779368;G:3248651209;T:3687437813;N:3180856 80 80     3747242594 3041779368 3248651209 3687437813 3180856 ERX7289612 ERS9293378 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.90779 0.9111 0.34976 0.34957 0.72827 0.73499 0.50071 0.49578 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10360 10360 ERR7720647 ERX7289611 ERS9293377 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 1dpa 2 SAMEA11646670 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646670|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:1dpa 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:1dpa 2|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:1dpa 2 p 1dpa 2 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 1dpa-2_1.fastq.gz 1dpa-2_2.fastq.gz fastq fastq 12524780320.0 78279877.0 E MTAB 7464 2:1dpa 2 0:80 1:80 A:3452368285;C:2754592593;G:2905324477;T:3409605329;N:2889636 80 80     3452368285 2754592593 2905324477 3409605329 2889636 ERX7289611 ERS9293377 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.90773 0.91019 0.32749 0.32608 0.73756 0.74172 0.51153 0.50818 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system
10361 10361 ERR7720646 ERX7289610 ERS9293376 ERP133910 PRJEB49404 Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E-MTAB-7464_2 Transcriptome Analysis Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes. ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 1dpa 1 SAMEA11646669 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646669|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:1dpa 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:1dpa 1|strain:AB                 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model E MTAB 7464 2:1dpa 1 p 1dpa 1 p Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model Following NCP treatment caudal fins of individuals were collected for each group control 1 dpa 7 dpa nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/ were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma A5040 25G then once fish were immobilized the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   ERP133910 NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 1dpa-1_1.fastq.gz 1dpa-1_2.fastq.gz fastq fastq 15395445120.0 96221532.0 E MTAB 7464 2:1dpa 1 0:80 1:80 A:4187891415;C:3447519966;G:3632085998;T:4124408897;N:3538844 80 80     4187891415 3447519966 3632085998 4124408897 3538844 ERX7289610 ERS9293376 ERA7895107 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.90197 0.907 0.33556 0.33653 0.73724 0.74546 0.51071 0.50585 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2022-12-29 Adult Adult Multi-tissue Multi-system

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;