metadata: run_metadata: 42 rows where devstage_curation_coarse = "Undetermined" and experiment.library

42 rows where devstage_curation_coarse = "Undetermined" and experiment.library_selection = "other"

descending

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.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	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.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	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
30210	30210	SRR27722348	SRX23388314	SRS20249507	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					2 F5 NPs	isolate:b1 F5\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	2 F5 NPs	2 F5 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701134_L1EGI0701134--WT_M5.R1.raw.fastq.gz L1EGI0701134_L1EGI0701134--WT_M5.R2.raw.fastq.gz	fastq fastq	6858985646.0	22711873.0	L1EGI0701134 L1EGI0701134 WT M5.R1.raw.fastq.gz	0:151 1:151	A:1775374486;C:1607590004;G:1736749854;T:1739241353;N:29949	151	151	1775374486	1607590004	1736749854	1739241353	29949	SRX23388314	SRS20249507	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30211	30211	SRR27722349	SRX23388313	SRS20249506	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					2 F4 NPs	isolate:b1 F4\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	2 F4 NPs	2 F4 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701133--WT_M4.R1.raw.fastq.gz L1EGI0701133--WT_M4.R2.raw.fastq.gz	fastq fastq	8367706978.0	27707639.0	L1EGI0701133 WT M4.R1.raw.fastq.gz	0:151 1:151	A:2190978299;C:1972956945;G:2068607164;T:2135130434;N:34136	151	151	2190978299	1972956945	2068607164	2135130434	34136	SRX23388313	SRS20249506	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30212	30212	SRR27722350	SRX23388312	SRS20249505	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					2 F3 NPs	isolate:b1 F3\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	2 F3 NPs	2 F3 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701132--WT_M3.R1.raw.fastq.gz L1EGI0701132--WT_M3.R2.raw.fastq.gz	fastq fastq	8356526334.0	27670617.0	L1EGI0701132 WT M3.R1.raw.fastq.gz	0:151 1:151	A:2162579680;C:1984443655;G:2083109306;T:2126359754;N:33939	151	151	2162579680	1984443655	2083109306	2126359754	33939	SRX23388312	SRS20249505	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30213	30213	SRR27722351	SRX23388311	SRS20249504	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					2 F2 NPs	isolate:b1 F2\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	2 F2 NPs	2 F2 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701131--WT_M2.R1.raw.fastq.gz L1EGI0701131--WT_M2.R2.raw.fastq.gz	fastq fastq	8143546874.0	26965387.0	L1EGI0701131 WT M2.R1.raw.fastq.gz	0:151 1:151	A:2114633540;C:1938964033;G:2015877300;T:2074038855;N:33146	151	151	2114633540	1938964033	2015877300	2074038855	33146	SRX23388311	SRS20249504	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30214	30214	SRR27722352	SRX23388310	SRS20249503	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					2 F1 NPs	isolate:b1 F1\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	2 F1 NPs	2 F1 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701130--WT_M1.R1.raw.fastq.gz L1EGI0701130--WT_M1.R2.raw.fastq.gz	fastq fastq	9004594174.0	29816537.0	L1EGI0701130 WT M1.R1.raw.fastq.gz	0:151 1:151	A:2356139884;C:2114457727;G:2228436842;T:2305522562;N:37159	151	151	2356139884	2114457727	2228436842	2305522562	37159	SRX23388310	SRS20249503	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30215	30215	SRR27722353	SRX23388309	SRS20249502	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					1 F5 WT	isolate:b1 F5\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	1 F5 WT	1 F5 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701128--WT_F5.R1.raw.fastq.gz L1EGI0701128--WT_F5.R2.raw.fastq.gz	fastq fastq	9595399794.0	31772847.0	L1EGI0701128 WT F5.R1.raw.fastq.gz	0:151 1:151	A:2471647902;C:2293433569;G:2400056012;T:2430223486;N:38825	151	151	2471647902	2293433569	2400056012	2430223486	38825	SRX23388309	SRS20249502	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30216	30216	SRR27722354	SRX23388308	SRS20249501	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					1 F4 WT	isolate:b1 F4\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	1 F4 WT	1 F4 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701127--WT_F4.R1.raw.fastq.gz L1EGI0701127--WT_F4.R2.raw.fastq.gz	fastq fastq	7628679456.0	25260528.0	L1EGI0701127 WT F4.R1.raw.fastq.gz	0:151 1:151	A:2006324404;C:1789150133;G:1873940582;T:1959232617;N:31720	151	151	2006324404	1789150133	1873940582	1959232617	31720	SRX23388308	SRS20249501	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30217	30217	SRR27722355	SRX23388307	SRS20249500	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					1 F3 WT	isolate:b1 F3\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	1 F3 WT	1 F3 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701126--WT_F3.R1.raw.fastq.gz L1EGI0701126--WT_F3.R2.raw.fastq.gz	fastq fastq	8853107954.0	29314927.0	L1EGI0701126 WT F3.R1.raw.fastq.gz	0:151 1:151	A:2281668777;C:2122390553;G:2205818678;T:2243193679;N:36267	151	151	2281668777	2122390553	2205818678	2243193679	36267	SRX23388307	SRS20249500	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30218	30218	SRR27722356	SRX23388306	SRS20249499	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					4 M5 NPs	isolate:b1 M5\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	4 M5 NPs	4 M5 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701146--NPs_M5.R1.raw.fastq.gz L1EGI0701146--NPs_M5.R2.raw.fastq.gz	fastq fastq	7440341686.0	24636893.0	L1EGI0701146 NPs M5.R1.raw.fastq.gz	0:151 1:151	A:1926837197;C:1774447312;G:1865805171;T:1873221668;N:30338	151	151	1926837197	1774447312	1865805171	1873221668	30338	SRX23388306	SRS20249499	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30219	30219	SRR27722357	SRX23388305	SRS20249498	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					4 M4 NPs	isolate:b1 M4\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	4 M4 NPs	4 M4 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701145_L1EGI0701145--NPs_M4.R1.raw.fastq.gz L1EGI0701145_L1EGI0701145--NPs_M4.R2.raw.fastq.gz	fastq fastq	7482324518.0	24775909.0	L1EGI0701145 L1EGI0701145 NPs M4.R1.raw.fastq.gz	0:151 1:151	A:2074937139;C:1646093888;G:1749156387;T:2012102736;N:34368	151	151	2074937139	1646093888	1749156387	2012102736	34368	SRX23388305	SRS20249498	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30220	30220	SRR27722358	SRX23388304	SRS20249497	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					4 M3 NPs	isolate:b1 M3\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	4 M3 NPs	4 M3 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701144--NPs_M3.R1.raw.fastq.gz L1EGI0701144--NPs_M3.R2.raw.fastq.gz	fastq fastq	8439432280.0	27945140.0	L1EGI0701144 NPs M3.R1.raw.fastq.gz	0:151 1:151	A:2168219326;C:2022693060;G:2132822366;T:2115662612;N:34916	151	151	2168219326	2022693060	2132822366	2115662612	34916	SRX23388304	SRS20249497	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30221	30221	SRR27722359	SRX23388303	SRS20249496	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					4 M2 NPs	isolate:b1 M2\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	4 M2 NPs	4 M2 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701143--NPs_M2.R1.raw.fastq.gz L1EGI0701143--NPs_M2.R2.raw.fastq.gz	fastq fastq	7033808614.0	23290757.0	L1EGI0701143 NPs M2.R1.raw.fastq.gz	0:151 1:151	A:1828789906;C:1675914023;G:1760006026;T:1769068832;N:29827	151	151	1828789906	1675914023	1760006026	1769068832	29827	SRX23388303	SRS20249496	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30222	30222	SRR27722360	SRX23388302	SRS20249495	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					4 M1 NPs	isolate:b1 M1\|host:male\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	4 M1 NPs	4 M1 NPs	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701142--NPs_M1.R1.raw.fastq.gz L1EGI0701142--NPs_M1.R2.raw.fastq.gz	fastq fastq	8087463964.0	26779682.0	L1EGI0701142 NPs M1.R1.raw.fastq.gz	0:151 1:151	A:2097695704;C:1931279917;G:2029894750;T:2028560473;N:33120	151	151	2097695704	1931279917	2029894750	2028560473	33120	SRX23388302	SRS20249495	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30223	30223	SRR27722361	SRX23388301	SRS20249494	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					3 M5 WT	isolate:b1 M5\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	3 M5 WT	3 M5 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701140--NPs_F5.R1.raw.fastq.gz L1EGI0701140--NPs_F5.R2.raw.fastq.gz	fastq fastq	8478344376.0	28073988.0	L1EGI0701140 NPs F5.R1.raw.fastq.gz	0:151 1:151	A:2202734913;C:2015133130;G:2106431143;T:2154009977;N:35213	151	151	2202734913	2015133130	2106431143	2154009977	35213	SRX23388301	SRS20249494	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30224	30224	SRR27722362	SRX23388300	SRS20249493	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					3 M4 WT	isolate:b1 M4\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	3 M4 WT	3 M4 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701139--NPs_F4.R1.raw.fastq.gz L1EGI0701139--NPs_F4.R2.raw.fastq.gz	fastq fastq	8569883596.0	28377098.0	L1EGI0701139 NPs F4.R1.raw.fastq.gz	0:151 1:151	A:2215047248;C:2038336388;G:2145335785;T:2171128844;N:35331	151	151	2215047248	2038336388	2145335785	2171128844	35331	SRX23388300	SRS20249493	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30225	30225	SRR27722363	SRX23388299	SRS20249492	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					3 M3 WT	isolate:b1 M3\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	3 M3 WT	3 M3 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701138--NPs_F3.R1.raw.fastq.gz L1EGI0701138--NPs_F3.R2.raw.fastq.gz	fastq fastq	7930364168.0	26259484.0	L1EGI0701138 NPs F3.R1.raw.fastq.gz	0:151 1:151	A:2046759305;C:1898600276;G:1959125241;T:2025847086;N:32260	151	151	2046759305	1898600276	1959125241	2025847086	32260	SRX23388299	SRS20249492	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30226	30226	SRR27722364	SRX23388298	SRS20249491	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					3 M2 WT	isolate:b1 M2\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	3 M2 WT	3 M2 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701137--NPs_F2.R1.raw.fastq.gz L1EGI0701137--NPs_F2.R2.raw.fastq.gz	fastq fastq	6914965272.0	22897236.0	L1EGI0701137 NPs F2.R1.raw.fastq.gz	0:151 1:151	A:1789644342;C:1644676301;G:1738643678;T:1741972870;N:28081	151	151	1789644342	1644676301	1738643678	1741972870	28081	SRX23388298	SRS20249491	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30227	30227	SRR27722365	SRX23388297	SRS20249490	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					3 M1 WT	isolate:b1 M1\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	3 M1 WT	3 M1 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701136--NPs_F1.R1.raw.fastq.gz L1EGI0701136--NPs_F1.R2.raw.fastq.gz	fastq fastq	7957071840.0	26347920.0	L1EGI0701136 NPs F1.R1.raw.fastq.gz	0:151 1:151	A:2056500264;C:1899503313;G:1979706436;T:2021329536;N:32291	151	151	2056500264	1899503313	1979706436	2021329536	32291	SRX23388297	SRS20249490	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30228	30228	SRR27722366	SRX23388296	SRS20249489	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					1 F2 WT	isolate:b1 F2\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	1 F2 WT	1 F2 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701125--WT_F2.R1.raw.fastq.gz L1EGI0701125--WT_F2.R2.raw.fastq.gz	fastq fastq	7960683760.0	26359880.0	L1EGI0701125 WT F2.R1.raw.fastq.gz	0:151 1:151	A:2087534093;C:1862286963;G:1962292721;T:2048536454;N:33529	151	151	2087534093	1862286963	1962292721	2048536454	33529	SRX23388296	SRS20249489	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
30229	30229	SRR27722367	SRX23388295	SRS20249488	SRP485828	PRJNA1068830	skeletal toxicity studies of polystyrene nanoplastic in zebrafish	PRJNA1068830	Other	Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.					1 F1 WT	isolate:b1 F1\|host:female\|collection date:2022 09 06\|geo loc name:China:qingdao\|tissue:b1\|BioSampleModel:Invertebrate							skeletal toxicity studies of polystyrene nanoplastic in zebrafish	1 F1 WT	1 F1 WT	bone			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP485828			L1EGI0701124--WT_F1.R1.raw.fastq.gz L1EGI0701124--WT_F1.R2.raw.fastq.gz	fastq fastq	8373285522.0	27726111.0	L1EGI0701124 WT F1.R1.raw.fastq.gz	0:151 1:151	A:2148645285;C:1996284185;G:2121066399;T:2107255525;N:34128	151	151	2148645285	1996284185	2121066399	2107255525	34128	SRX23388295	SRS20249488	SRA1791477	zhejiang university\|the college of animal science	zhejiang university												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-01-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
33123	33123	SRR29672615	SRX25176099	SRS21866000	SRP517393	PRJNA1130538	ac4C transcriptomes of Zebrafish and Worm	GSE271258	Other	ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution we performed ac4C RIP seq on Zebrafish and Worm.				Zebrafish ac4C	GSM8372406	tissue:Animal organ cells\|cell type:Animal organ cells\|genotype:Wild type\|rip antibody:anti ac4C Abcam catalog No. ab252215\|geo loc name:missing\|collection date:missing	Zebrafish ac4C	The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2 and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq the mRNA expression level was analyzed by StringTie and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format containing the expression levels and ac4C status changes for each gene.	Animal organ cells	Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched	cell type:Animal organ cells\|genotype:Wild type\|rip antibody:anti ac4C Abcam catalog No. ab252215	GSM8372406	GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq	GSM8372406 r1	GSM8372406	1	Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP517393			Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz	fastq fastq	816231517.0	3830403.0	GSM8372406 r1	0:102.34 1:110.76	A:199381841;C:207571478;G:205740791;T:203535549;N:1858	102	110	199381841	207571478	205740791	203535549	1858	SRX25176099	SRS21866000	SRA1914369	Fujian Medical University	Fujian Medical University	2	0.60415	0.60545	0.08824	0.08794	0.78796	0.78733	0.43432	0.43842	126	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-07-01	Undetermined	Undetermined	Undetermined	Undetermined
36285	36285	SRR363985	SRX105298	SRS270141	SRP009275	PRJNA148581	Hen1 analysis in zebrafish	GSE33582	Transcriptome Analysis	small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.		pubmed:20859253		wildtype ligation	GSM830247	source name:testis\|strain:TL\|genotype/variation:Hen1 wildtype\|tissue:testis\|small rna library prep method:adapter ligation	wildtype ligation	three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8	testis	Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.	strain:TL\|genotype/variation:Hen1 wildtype\|tissue:testis\|small rna library prep method:adapter ligation	GSM830247	GSM830247: wildtype ligation	GSM830247: wildtype ligation	GSM830247: wildtype ligation	1		GEO Accession:GSM830247	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP009275		read name barcode proc directive:ignore	WTTESTIS.fastq	fastq	395791130.0	8604155.0	GSM830247 1	0:46	A:79045664;C:90489917;G:99082007;T:127024229;N:149313	46		79045664	90489917	99082007	127024229	149313	SRX105298	SRS270141	SRA047996	GEO	European Research Institute for the Biology of Ageing, University Medical Center Groningen	1	0.00021		0.00015		0.99989		0.0		46		T		under 1.2% mapping rate	illumina	early_illumina	5prime	poly_a	unknown	bulk	unknown	unknown	Netherlands	2011-11-09	Undetermined	Undetermined	Gonad	Reproductive System
36286	36286	SRR363984	SRX105297	SRS270140	SRP009275	PRJNA148581	Hen1 analysis in zebrafish	GSE33582	Transcriptome Analysis	small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.		pubmed:20859253		hen1 mutant ligation	GSM830246	source name:testis\|strain:TL\|genotype/variation:Hen1 mutant\|tissue:testis\|small rna library prep method:adapter ligation	hen1 mutant ligation	three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8	testis	Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.	strain:TL\|genotype/variation:Hen1 mutant\|tissue:testis\|small rna library prep method:adapter ligation	GSM830246	GSM830246: hen1 mutant ligation	GSM830246: hen1 mutant ligation	GSM830246: hen1 mutant ligation	1		GEO Accession:GSM830246	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP009275		read name barcode proc directive:ignore	HEN1TESTIS.fastq	fastq	440876374.0	9584269.0	GSM830246 1	0:46	A:91693980;C:99515953;G:105634029;T:143841954;N:190458	46		91693980	99515953	105634029	143841954	190458	SRX105297	SRS270140	SRA047996	GEO	European Research Institute for the Biology of Ageing, University Medical Center Groningen	1	0.00039		0.00033		0.99995		0.0		46		T		under 1.2% mapping rate	illumina	early_illumina	5prime	poly_a	unknown	bulk	unknown	unknown	Netherlands	2011-11-09	Undetermined	Undetermined	Gonad	Reproductive System
36287	36287	SRR363983	SRX105296	SRS270139	SRP009275	PRJNA148581	Hen1 analysis in zebrafish	GSE33582	Transcriptome Analysis	small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.		pubmed:20859253		wildtype polyA	GSM830245	source name:testis\|strain:TL\|genotype/variation:Hen1 wildtype\|tissue:testis\|small rna library prep method:polyA tailing	wildtype polyA	three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8	testis	Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.	strain:TL\|genotype/variation:Hen1 wildtype\|tissue:testis\|small rna library prep method:polyA tailing	GSM830245	GSM830245: wildtype polyA	GSM830245: wildtype polyA	GSM830245: wildtype polyA	1		GEO Accession:GSM830245	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP009275		read name barcode proc directive:ignore	VASAGFPHEN1plusMALE.fastq	fastq	167344144.0	3803276.0	GSM830245 1	0:44	A:87935982;C:21182538;G:19081938;T:34474815;N:4668871	44		87935982	21182538	19081938	34474815	4668871	SRX105296	SRS270139	SRA047996	GEO	European Research Institute for the Biology of Ageing, University Medical Center Groningen	1	0.06642		0.05042		0.99226		0.38346		44		B		usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	Netherlands	2011-11-09	Undetermined	Undetermined	Gonad	Reproductive System
50795	50795	SRR8305648	SRX5120118	SRS4121998	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.		pubmed:30597924	Replicate 3		14dpi#3	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#3\|BioSampleModel:Model organism or animal							14dpi rep3 miRNA	6011	6011	miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP173044			SID6011_S15_L003_R1_001.fastq.gz	fastq	578164050.0	11563281.0	SID6011 S15 L003 R1 001.fastq.gz	0:50	A:109934197;C:149003532;G:179264553;T:139924815;N:36953	50		109934197	149003532	179264553	139924815	36953	SRX5120118	SRS4121998	SRA822004	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	1	0.0225		0.00372		0.9906		0.61747		50		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	unknown	unknown	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
50796	50796	SRR8305649	SRX5120117	SRS4121996	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.		pubmed:30597924	Replicate 2		14dpi#2	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#2\|BioSampleModel:Model organism or animal							14dpi rep2 miRNA	6010	6010	miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP173044			SID6010_S14_L003_R1_001.fastq.gz	fastq	682820200.0	13656404.0	SID6010 S14 L003 R1 001.fastq.gz	0:50	A:132413613;C:177691857;G:213067602;T:159602931;N:44197	50		132413613	177691857	213067602	159602931	44197	SRX5120117	SRS4121996	SRA822004	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	1	0.02361		0.00321		0.99281		0.46548		50		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	unknown	unknown	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
50797	50797	SRR8305650	SRX5120116	SRS4121997	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.		pubmed:30597924	Replicate 1		14dpi#1	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#1\|BioSampleModel:Model organism or animal							14dpi rep1 miRNA	6009	6009	miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP173044			SID6009_S5_L006_R1_001.fastq.gz	fastq	645018650.0	12900373.0	SID6009 S5 L006 R1 001.fastq.gz	0:50	A:121217579;C:170403284;G:199790376;T:153583951;N:23460	50		121217579	170403284	199790376	153583951	23460	SRX5120116	SRS4121997	SRA822004	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	1	0.02637		0.00359		0.99095		0.50364		50		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	unknown	unknown	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
50816	50816	SRR8298682	SRX5113200	SRS4121998	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.		pubmed:30597924	Replicate 3		14dpi#3	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#3\|BioSampleModel:Model organism or animal							14dpi rep3	5946	5946	RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP173044			SID5946_S35_L007_R1_001.fastq.gz SID5946_S35_L007_R2_001.fastq.gz	fastq fastq	4648725300.0	30991502.0	SID5946 S35 L007 R1 001.fastq.gz	0:75 1:75	A:1303485934;C:1019161225;G:1015495862;T:1308163547;N:2418732	75	75	1303485934	1019161225	1015495862	1308163547	2418732	SRX5113200	SRS4121998	SRA821074	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	2	0.92153	0.92446	0.28679	0.28712	0.77792	0.78042	0.57131	0.56895	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	bulk	bulk	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
50818	50818	SRR8298684	SRX5113198	SRS4121997	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.		pubmed:30597924	Replicate 1		14dpi#1	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#1\|BioSampleModel:Model organism or animal							14dpi rep1	5944	5944	RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP173044			SID5944_S33_L007_R1_001.fastq.gz SID5944_S33_L007_R2_001.fastq.gz	fastq fastq	4880230050.0	32534867.0	SID5944 S33 L007 R1 001.fastq.gz	0:75 1:75	A:1375786208;C:1064869277;G:1049678552;T:1387347217;N:2548796	75	75	1375786208	1064869277	1049678552	1387347217	2548796	SRX5113198	SRS4121997	SRA821074	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	2	0.92418	0.92876	0.27259	0.27339	0.78526	0.78888	0.57372	0.57769	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	bulk	bulk	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
50819	50819	SRR8298685	SRX5113197	SRS4121996	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.		pubmed:30597924	Replicate 2		14dpi#2	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#2\|BioSampleModel:Model organism or animal							14dpi rep2	5945	5945	RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP173044			SID5945_S34_L007_R1_001.fastq.gz SID5945_S34_L007_R2_001.fastq.gz	fastq fastq	4722657450.0	31484383.0	SID5945 S34 L007 R1 001.fastq.gz	0:75 1:75	A:1318733900;C:1041426176;G:1033500671;T:1326546335;N:2450368	75	75	1318733900	1041426176	1033500671	1326546335	2450368	SRX5113197	SRS4121996	SRA821074	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	2	0.92723	0.92976	0.27077	0.27133	0.76232	0.76451	0.57825	0.57723	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	bulk	bulk	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
62700	62700	SRR13327930	SRX9755046	SRS7944756	SRP299775	PRJNA688655	RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	PRJNA688655	Other					Mut 0h k3	Mut 0h k3	strain:AB\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:11\|dev stage:mission\|sex:not collected\|tissue:kidney and headkidney\|biomaterial provider:Southwest University China\|replicate:Biological replicate 3\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	Mut 0h k3	Mut k3	other			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten		SRP299775			WT_0h_k3.raw_1.fastq.gz WT_0h_k3.raw_2.fastq.gz	fastq fastq	6675348000.0	22251160.0	WT 0h k3.raw 1.fastq.gz	0:150 1:150	A:1848988411;C:1470625677;G:1544465916;T:1811246237;N:21759	150	150	1848988411	1470625677	1544465916	1811246237	21759	SRX9755046	SRS7944756	SRA1178968	southwest university\|college of fisheries	southwest university	2	0.86263	0.92706	0.08978	0.0978	0.70502	0.69895	0.55273	0.55505	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-12-30	Undetermined	Undetermined	Kidney	Renal System
62701	62701	SRR13327931	SRX9755045	SRS7944755	SRP299775	PRJNA688655	RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	PRJNA688655	Other					Mut 0h k2	Mut 0h k2	strain:AB\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:10\|dev stage:mission\|sex:not collected\|tissue:kidney and headkidney\|biomaterial provider:Southwest University China\|replicate:Biological replicate 2\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	Mut 0h k2	Mut k2	other			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten		SRP299775			WT_0h_k2.raw_1.fastq.gz WT_0h_k2.raw_2.fastq.gz	fastq fastq	7165537800.0	23885126.0	WT 0h k2.raw 1.fastq.gz	0:150 1:150	A:1961366053;C:1599856726;G:1683336568;T:1920956264;N:22189	150	150	1961366053	1599856726	1683336568	1920956264	22189	SRX9755045	SRS7944755	SRA1178968	southwest university\|college of fisheries	southwest university	2	0.93437	0.93173	0.09166	0.09117	0.6997	0.70031	0.5364	0.53886	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-12-30	Undetermined	Undetermined	Kidney	Renal System
62702	62702	SRR13327932	SRX9755044	SRS7944754	SRP299775	PRJNA688655	RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	PRJNA688655	Other					Mut 0h k1	Mut 0h k1	strain:AB\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:9\|dev stage:mission\|sex:not collected\|tissue:kidney and headkidney\|biomaterial provider:Southwest University China\|replicate:Biological replicate 1\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	Mut 0h k1	Mut k1	other			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten		SRP299775			WT_0h_k1.raw_1.fastq.gz WT_0h_k1.raw_2.fastq.gz	fastq fastq	5953238400.0	19844128.0	WT 0h k1.raw 1.fastq.gz	0:150 1:150	A:1643432335;C:1323053555;G:1377906382;T:1608824934;N:21194	150	150	1643432335	1323053555	1377906382	1608824934	21194	SRX9755044	SRS7944754	SRA1178968	southwest university\|college of fisheries	southwest university	2	0.93408	0.93293	0.08519	0.08534	0.70952	0.71029	0.56062	0.52712	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-12-30	Undetermined	Undetermined	Kidney	Renal System
62703	62703	SRR13327933	SRX9755043	SRS7944753	SRP299775	PRJNA688655	RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	PRJNA688655	Other					WT 0h k3	WT 0h k3	strain:AB\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:8\|dev stage:mission\|sex:not collected\|tissue:kidney and headkidney\|biomaterial provider:Southwest University China\|replicate:Biological replicate 3\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	WT 0h k3	WT k3	other			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten		SRP299775			Mut_0h_k3.raw_1.fastq.gz Mut_0h_k3.raw_2.fastq.gz	fastq fastq	5891495100.0	19638317.0	Mut 0h k3.raw 1.fastq.gz	0:150 1:150	A:1626936306;C:1303639063;G:1370950045;T:1589948552;N:21134	150	150	1626936306	1303639063	1370950045	1589948552	21134	SRX9755043	SRS7944753	SRA1178968	southwest university\|college of fisheries	southwest university	2	0.93117	0.93006	0.09742	0.09724	0.70396	0.7041	0.53898	0.53936	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-12-30	Undetermined	Undetermined	Kidney	Renal System
62704	62704	SRR13327934	SRX9755042	SRS7944752	SRP299775	PRJNA688655	RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	PRJNA688655	Other					WT 0h k2	WT 0h k2	strain:AB\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7\|dev stage:mission\|sex:not collected\|tissue:kidney and headkidney\|biomaterial provider:Southwest University China\|replicate:Biological replicate 2\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	WT 0h k2	WT k2	other			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten		SRP299775			Mut_0h_k2.raw_1.fastq.gz Mut_0h_k2.raw_2.fastq.gz	fastq fastq	5543211000.0	18477370.0	Mut 0h k2.raw 1.fastq.gz	0:150 1:150	A:1531314014;C:1225009325;G:1291427420;T:1495440150;N:20091	150	150	1531314014	1225009325	1291427420	1495440150	20091	SRX9755042	SRS7944752	SRA1178968	southwest university\|college of fisheries	southwest university	2	0.93219	0.93172	0.10466	0.10531	0.70141	0.70104	0.53257	0.53162	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-12-30	Undetermined	Undetermined	Kidney	Renal System
62705	62705	SRR13327935	SRX9755041	SRS7944751	SRP299775	PRJNA688655	RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	PRJNA688655	Other					WT 0h k1	WT 0h k1	strain:AB\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:6\|dev stage:mission\|sex:not collected\|tissue:kidney and headkidney\|biomaterial provider:Southwest University China\|replicate:Biological replicate 1\|BioSampleModel:Model organism or animal							RNA Seq of Danio rerio: kidney and headkidney from wild type and congenitally asplenic zebrafish	WT 0h k1	WT k1	other			RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten		SRP299775			Mut_0h_k1.raw_1.fastq.gz Mut_0h_k1.raw_2.fastq.gz	fastq fastq	6954804600.0	23182682.0	Mut 0h k1.raw 1.fastq.gz	0:150 1:150	A:1929335607;C:1531367791;G:1605966700;T:1888112325;N:22177	150	150	1929335607	1531367791	1605966700	1888112325	22177	SRX9755041	SRS7944751	SRA1178968	southwest university\|college of fisheries	southwest university	2	0.9401	0.93841	0.08725	0.08725	0.71536	0.71569	0.56381	0.56397	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-12-30	Undetermined	Undetermined	Kidney	Renal 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");;