run_metadata: 46218
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 46218 | SRR6506180 | SRX3594764 | SRS2867189 | SRP131362 | PRJNA431371 | Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and smyd4 mutant zebrafish cardiac transcriptomes | GSE109553 | Transcriptome Analysis | Heart tissue mRNA profiles of 50 wild type WT and 50 homozygous smyd4 mutant zebrafish embryos at 72 hpf created by CRISPR/Cas9 were generated by deep sequencing. Overall design: Heart mRNA profiles of 72 hpf wild type WT and smdy4 mutant zebrafish were generated by deep sequencing using illumina | wt | GSM2946170 | source name:heart|tissue:heart|strain:Tu|age:72 hpf|genotype:wt | wt | Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Bowtie v2.0.6 and paired end clean reads were aligned to the reference genome using TopHat v2.0.9. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene considering the effect of sequencing depth and gene length for the reads count at the same time Mortazavi et al. 2008 Genome build: ftp://ftp.ensembl.org/pub/release 89/fasta/danio rerio/dna/ Supplementary files format and content: text file with RPKM | heart | zebrafish heart were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:heart|strain:Tu|age:72 hpf|genotype:wt | GSM2946170 | GSM2946170: wt; Danio rerio; RNA Seq | GSM2946170 | 1 | zebrafish heart were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM2946170 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP131362 | ctr_zf_1.fq.gz ctr_zf_2.fq.gz | fastq fastq | 9601941900.0 | 32006473.0 | GSM2946170 r1 | 0:150 1:150 | A:2440007788;C:2202792595;G:2248095757;T:2709447485;N:1598275 | 150 | 150 | 2440007788 | 2202792595 | 2248095757 | 2709447485 | 1598275 | SRX3594764 | SRS2867189 | SRA651951 | GEO | Fudan university | 2 | 0.93538 | 0.92842 | 0.05404 | 0.04218 | 0.7387 | 0.75866 | 0.43777 | 0.42189 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2018-01-24 | Larval | Larval | Heart | Cardiovascular System |