run_metadata: 39740
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 39740 | SRR2087763 | SRX1081749 | SRS979503 | SRP060373 | PRJNA288987 | RNA Seq matched to ribosome profiling over a zebrafish developmental timecourse | GSE70549 | Transcriptome Analysis | RNA Seq data that is sample matched to a previous ribosome profiling dataset GSE46512 Overall design: RNA Seq over 8 stages in early zebrafish development matched to ribosome profiling data in : 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf | 2012 07 26 2 4Cell | GSM1808905 | tissue:Whole embryos|developmental stage:2 4 cells|strain:TL/AB | 2012 07 26 2 4Cell | Aligned using Tophat2 with supplied transcript junctions from Ensembl 72 Timecourse quantified with Cufflinks on Ensembl 72 transcripts Genome build: danRer7/Zv9 Supplementary files format and content: genes.fpkm tracking from cufflinks for gene expression quantification at loci level FPKM | Whole embryos | Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen | Total RNA was isolated using the standard TRIzol Invitrogen protocol. Genomic DNA was removed by DNase treatment. Two rounds of PolyA+ RNA purification were performed for each sample. Strand specific libraries for 76 bp paired end sequencing were prepared according to a modified UTP method Parkhomchuk et al. 2009 as detailed by Levin et al. 2010. Libraries were sequenced on the Illumina HiSeq 2000 | 100 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995 | developmental stage:2 4 cells|strain:TL/AB | GSM1808905 | GSM1808905: 2012 07 26 2 4Cell; Danio rerio; RNA Seq | GSM1808905 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol. Genomic DNA was removed by DNase treatment. Two rounds of PolyA+ RNA purification were performed for each sample. Strand specific libraries for 76 bp paired end sequencing were prepared according to a modified UTP method Parkhomchuk et al. 2009 as detailed by Levin et al. 2010. Libraries were sequenced on the Illumina HiSeq 2000 | GEO Accession:GSM1808905 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP060373 | RPF-RNASeq_2-4Cell_3.bam | bam | 2221368432.0 | 14614266.0 | GSM1808905 r3 | 0:76 1:76 | A:583022149;C:529325209;G:538117340;T:569984927;N:918807 | 76 | 76 | 583022149 | 529325209 | 538117340 | 569984927 | 918807 | SRX1081749 | SRS979503 | SRA275803 | GEO | Schier, Dept of Molecular and Cellular Biology, Harvard University | 2 | 0.94898 | 0.95604 | 0.0573 | 0.05616 | 0.78973 | 0.79147 | 0.49226 | 0.48034 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2015-07-06 | Cleavage | Embryo | Whole Organism | All anatomical structures |