run_metadata: 42249

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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
42249	SRR5507584	SRX2783295	SRS2165432	SRP106454	PRJNA385396	Parental exposure to gamma radiation causes progressively altered transcriptomes that are linked to adverse effects in zebrafish offspring	GSE98539	Transcriptome Analysis	In zebrafish parental exposure to ionizing radiation has been associated with effects in offspring such as increased DNA damage and reactive oxygen species. Here we assessed short one month and long term effects one year on gene expression in embryonic offspring 5.5 hpf from zebrafish exposed during gametogenesis to gamma radiation 8.7 or 53 mGy/h for 27 days total dose 5.2 or 31 Gy. One month post exposure a global change in gene expression was observed in offspring from the 53 mGy/h group followed by embryonic death at late gastrula whereas offspring from the 8.7 mGy/h group was unaffected. One year post exposure embryos from the 8.7 mGy/h group exhibited 245561.8% downregulated differentially expressed genes. Overlaps in differentially expressed genes and enriched biological pathways were evident between the 53 mGy/h group one month and 8.7 mGy/h one year post exposure which could be linked to effects in adults and offspring such as DNA damage and lipid peroxidation. Interestingly pathways between the two groups were oppositely regulated. Our results indicate latent effects following ionizing radiation exposure in parents that can be transmitted to offspring and warrants monitoring effects over subsequent generations. Overall design: One month post exposure mRNA from F1 5.5 hpf embryos from parents exposed to 8.7 and 53 mGy/h gamma radiation during gametogenesis was sequenced on the Illumina 4000 platform with three replicas per treatment. One year post exposure mRNA from F1 embryos from the same parents exposed to 8.7 mGy/h was sequenced with three biological replicates. In both cases F1 embryos from non exposed parents were used as control and mRNA sequenced in triplicates taken at the same time points as the exposed samples.		pubmed:29248853;pubmed:33602989		Nmbu RNA 14	GSM2598411		tissue:F1 embryos from exposed parents 8.7 mGy/h post 1y\|strain:AB wild type\|developmental stage:5.5 hpf	Nmbu RNA 14	Adaptor trimming using trim galore v0.4.2 with default parameters. Additional 1 base clipped from three prime end and 12 bases at five prime end in both pair of reads Quality analysis using FastQC v0.11.5. Only pair of reads with phred score of 20 or above were retained. Mapping using STAR aligner v2.5.2b. Visualization and mapping quality assessed with seqmonk v.1.35 using SAM files obtained from the step above. Gene expression was quantified using in build mRNA seq pipeline of seqmonk Differential expression was assessed using the in build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05 Genome build: GRCz10 Supplementary files format and content: mapping files in SAM format. Expression files: Count table matrix for all gene expressed. Count table matrix for all differentially expressed genes DEG. Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format .csv providing Chromosome name genome coordinate Ensembl transcript ID Gene symbol and description gene biotype per sample expression values as log2 of the normalized read count FDR.	F1 embryos from exposed parents 8.7 mGy/h post 1y	AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis F1 offspring was collected one month post exposure from control and exposed parents. post one year exposed only 8.7 mGy/h and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.	Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures’ instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 µl RNase free water and stored at − 80°C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 µg total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation’s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.		strain:AB wild type\|developmental stage:5.5 hpf	GSM2598411	GSM2598411: Nmbu RNA 14; Danio rerio; RNA Seq	GSM2598411		1	Total RNA was isolated with TRIzol Reagent Invitrogen according to manufactures’ instructions. Briefly 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads Roche Diagnostics. Each sample was eluted in 40 µl RNase free water and stored at − 80°C until required. RNA purity and yield was determined using NanoDrop 1000 Spectrophotometer NanoDrop Technologies Wilmington DE and RNA integrity number RIN was assessed with Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA using RNA Nano LabChip Kit Agilent Technologies which were all of sufficient quality for sequencing RIN > 9.0. One sample control 0 yr got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr. Per sample a total of 1.5 µg total RNA was used for library preparation. Non directional libraries were generated using the NEBNExt Ultra mRNA kit New England Biolabs USA according the manufacturers recommendation’s. mRNA was enriched using oligo dT beads followed by fragmentation followed by first strand cDNA synthesis using random hexamers and M MuLV reverse transcriptase. post first strand synthesis a custom second strand synthesis buffer Illumina is added with dNTPs RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated post a round of purification terminal repair A tailing ligation of sequencing adapters size selection and PCR enrichment. PCR products were purified with the AMPure XP system Beckman US and library quality was checked on the Agilent Bioanalyzer 2100 system Agilent US. Libraries were analyzed in paired end 150 bp on the Hiseq 4000 Illumina US using 150 bp paired end reads.	GEO Accession:GSM2598411	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP106454			nmbu-RNA-14_HL7MMCCXX_L4_1.fq.gz nmbu-RNA-14_HL7MMCCXX_L4_2.fq.gz	fastq fastq	5633328900.0	18777763.0	GSM2598411 r1	0:150 1:150	A:1412757538;C:1395215147;G:1427182503;T:1397831592;N:342120	150	150			1412757538	1395215147	1427182503	1397831592	342120	SRX2783295	SRS2165432	SRA559556	GEO	Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences	2	0.95017	0.94647	0.05539	0.05499	0.75556	0.75952	0.50736	0.51408	150	150	B	B	biological fallback assumption	illumina	hiseq_era	5prime	poly_a	nebnext	bulk	bulk	bulk		Norway	2017-05-04	Gastrula	Embryo	Embryo Imprecise	All anatomical structures