run_metadata: 59624
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 |
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| 59624 | SRR11974582 | SRX8518004 | SRS6815485 | SRP266770 | PRJNA638603 | small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish | GSE152189 | Transcriptome Analysis | In order to investigate transcriptomic mechanisms underlying radiation exposure we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ? and control F1 C parents revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall 22 miRNAs 11 piRNA clusters 19 snRNAs and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data a total of 672 differentially expressed mRNAs could be linked to the DEmiRs of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor NFkB and PTEN signaling linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group 68.8% of which were U1 and U2 snRNAs. In addition 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR LINE and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs indicating expression of DEpiRNAs in response to activation of TEs. Finally 66.7% and 33.3% of lincRNAs in F1 ? were down and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression. | pubmed:33602989 | F1 Gamma2 nmbu sncRNA 2 | GSM4605881 | tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents | F1 Gamma2 nmbu sncRNA 2 | Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped classified into genomic features and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5 using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values | Whole embryo | Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material. | develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents | GSM4605881 | GSM4605881: F1 Gamma2 nmbu sncRNA 2; Danio rerio; miRNA Seq | GSM4605881 | 1 | Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material. | GEO Accession:GSM4605881 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP266770 | nmbu_sncRNA_5_raw.fq.gz | fastq | 579779650.0 | 11595593.0 | GSM4605881 r1 | 0:50 | A:173232869;C:126599907;G:152751070;T:127092652;N:103152 | 50 | 173232869 | 126599907 | 152751070 | 127092652 | 103152 | SRX8518004 | SRS6815485 | SRA1085407 | GEO | Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences | 1 | 0.7644 | 0.48211 | 0.84583 | 0.59288 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | size_fractionation | nebnext | bulk | unknown | unknown | Norway | 2020-06-10 | Gastrula | Embryo | Whole Organism | All anatomical structures |