run_metadata: 51327
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 51327 | SRR8749827 | SRX5540805 | SRS4506467 | SRP188811 | PRJNA527965 | Loss of Pitx2c predisposes to arrhythmia and atrial fibrillation pathologies via structural and metabolic dysfunction | GSE128511 | Transcriptome Analysis | RNAseq profiling of embryonic zebrafish hearts was performed to identify differentially expressed genes downstream of Pitx2c. Overall design: Embryonic hearts were dissected from wild type pitx2c mutants and pitx2c gain of function OE embryos at 56 hpf | pubmed:31704768 | WT 1: wild type | GSM3678229 | source name:pools of 56 hpf hearts|tissue:embryonic heart|Stage:56 hpf|genotype/variation:wild type | WT 1: wild type | Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus Ensembl Zebrafish genome version DanRer10 GRCz10.87 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. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanRer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak | pools of 56 hpf hearts | Hearts were dissected from embryos in HBSS. RNA was isolated using miRNeasy micro kit QIAGEN with on column DNase digestion 5ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Takara Clontech. | Embryos were grown at 28C until 56 hpf | tissue:embryonic heart|Stage:56 hpf|genotype/variation:wild type | GSM3678229 | GSM3678229: WT 1: wild type; Danio rerio; RNA Seq | GSM3678229 | 1 | Hearts were dissected from embryos in HBSS. RNA was isolated using miRNeasy micro kit QIAGEN with on column DNase digestion 5ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Takara Clontech. | GEO Accession:GSM3678229 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP188811 | Collins_WT_1_R1.fastq | fastq | 2611972794.0 | 35734636.0 | GSM3678229 r1 | 0:73.09 1:0 | A:626940885;C:701243949;G:741441019;T:542275683;N:71258 | 73 | 0 | 626940885 | 701243949 | 741441019 | 542275683 | 71258 | SRX5540805 | SRS4506467 | SRA861990 | GEO | MPI for heart and lung research | 1 | 0.91014 | 0.26179 | 0.80547 | 0.70064 | 47 | B | usable mapping rate | illumina | nextseq | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | Germany | 2019-03-19 | Hatching | Embryo | Heart | Cardiovascular System |