run_metadata: 58970
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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| 58970 | SRR11575112 | SRX8143232 | SRS6506143 | SRP257532 | PRJNA626621 | Identification of target genes in tie1 mutant zebrafish heart by transcriptomic analysis | GSE148957 | Transcriptome Analysis | Purpose: identifying with RNA seq genes targets of Tie1 during the cardiac development in zebrafish. Results: we identified several differential expressed genes with an enrichment in ECM modulator genes. Overall design: Hearts were manually extracted at 48 hpf from tie1 mutants and wild type and heterozygous siblings. | tie1 WT 1 | GSM4486658 | source name:Tgkdrl:eGFP|tissue:Hearts|developmental stage:48 hpf|genotype:tie1 WT | tie1 WT 1 | The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC available online at http://www.bioinformatics.babraham.ac.uk/ projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides 6. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.4.0a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package 8. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer11 Supplementary files format and content: library size normalized counts | Tgkdrl:eGFP | Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles pooled in 1.5 ml tubes with TRIzol and frozen in 80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen. For exclusion of genomic DNA contamination the samples were treated by on column DNase digestion DNase Free DNase Set Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Takara Clontech. | tissue:Hearts|developmental stage:48 hpf|genotype:tie1 WT | GSM4486658 | GSM4486658: tie1 WT 1; Danio rerio; RNA Seq | GSM4486658 | 1 | Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles pooled in 1.5 ml tubes with TRIzol and frozen in 80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen. For exclusion of genomic DNA contamination the samples were treated by on column DNase digestion DNase Free DNase Set Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Takara Clontech. | GEO Accession:GSM4486658 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP257532 | Carlantoni_RNA_WT_1.fastq.gz | fastq | 1494085887.0 | 20050038.0 | GSM4486658 r1 | 0:74.52 1:0 | A:282811923;C:486533537;G:414513849;T:310220539;N:6039 | 74 | 0 | 282811923 | 486533537 | 414513849 | 310220539 | 6039 | SRX8143232 | SRS6506143 | SRA1067178 | GEO | MPI for heart and lung research | 1 | 0.9512 | 0.17902 | 0.89757 | 0.79881 | 75 | B | usable mapping rate | illumina | nextseq | full_length | cdna_unspecified | smarter | bulk | bulk | bulk | Germany | 2020-04-20 | Hatching | Embryo | Heart | Cardiovascular System |