run_metadata: 9867

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
9867	ERR4091977	ERX4087478	ERS4539480	ERP121491	PRJEB38108	RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS	E-MTAB-9018	Transcriptome Analysis	Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response.	ENA FIRST PUBLIC:2020 07 31\|ENA LAST UPDATE:2020 05 01		Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 μl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. ThenPCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.	Sample 4	SAMEA6811834	Centre of Marine Sciences	ENA FIRST PUBLIC:2020 07 31T04:03:56Z\|ENA LAST UPDATE:2020 05 01T13:37:30Z\|External Id:SAMEA6811834\|INSDC center name:Centre of Marine Sciences\|INSDC first public:2020 07 31T04:03:56Z\|INSDC last update:2020 05 01T13:37:30Z\|INSDC status:public\|Submitter Id:E MTAB 9018:Sample 4\|age:8\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:CRISPR/Cas9 mediated Sst3 / knockout\|individual:pool of 10 individuals 4\|sample name:E MTAB 9018:Sample 4\|scientific name:Danio rerio\|strain:AB									HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS	E MTAB 9018:Sample 4 p	Sample 4 p	RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS	Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 μl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. ThenPCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.	Experimental Factor: genotype:CRISPR/Cas9 mediated Sst3 / knockout\|Experimental Factor: stimulus:dextran sodium sulfate sodium 0.4%	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP121491	HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS	ENA FIRST PUBLIC:2020 07 31\|ENA LAST UPDATE:2020 05 01	M_DSS_A_1.fq.gz M_DSS_A_2.fq.gz	fastq fastq	7688293800.0	25627646.0	E MTAB 9018:M DSS A	0:150 1:150	A:2073022052;C:1791469708;G:1778836919;T:2044769558;N:195563	150	150			2073022052	1791469708	1778836919	2044769558	195563	ERX4087478	ERS4539480	ERA2539869	European Nucleotide Archive	European Nucleotide Archive	2	0.9469	0.94648	0.09843	0.09883	0.65646	0.65681	0.4755	0.47342	150	150	B	B	biological fallback assumption	illumina	hiseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown		Unknown	2020-05-01	Larval	Larval	Whole Organism	All anatomical structures