run_metadata: 39703
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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| 39703 | SRR2057604 | SRX1054376 | SRS957216 | SRP059278 | PRJNA286201 | MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome [miRNA seq] | GSE69690 | Transcriptome Analysis | The regulative role of miRNAs in Holt Oram Syndrome is investigated in a zebrafish model. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT sample. 1.5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxxhpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA286199 | pubmed:26657204 | Emb MO Ct 48hpf [miRNA seq] | GSM1707594 | source name:Embryos MO Ct 48hpf|strain background:AB|infected with:MO C|tissue:embryo|developmental stage:48hpf | Emb MO Ct 48hpf [miRNA seq] | Basecalls performed using GA Pipeline v1.5 Sequenced reads were filtered for low quality and trimmed for three prime adaptor sequence. Reads were algned to mirBase v16.0 using CLC workbench Expression values were normalized to reads per million rpm Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Ct 48hpf | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | strain background:AB|infected with:MO C|tissue:embryo|developmental stage:48hpf | GSM1707594 | GSM1707594: Emb MO Ct 48hpf [miRNA seq]; Danio rerio; miRNA Seq | GSM1707594 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1707594 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP059278 | Dre_FC_4.fq.gz | fastq | 1033068440.0 | 25826711.0 | GSM1707594 r1 | 0:40 | A:417902194;C:195580811;G:153264728;T:266159736;N:160971 | 40 | 417902194 | 195580811 | 153264728 | 266159736 | 160971 | SRX1054376 | SRS957216 | SRA272222 | GEO | IIT, CNR | 1 | 0.05412 | 0.01319 | 0.97693 | 0.22489 | 40 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2015-06-09 | Hatching | Embryo | Embryo Imprecise | All anatomical structures |