run_metadata: 39756
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 39756 | SRR2125736 | SRX1117105 | SRS1010315 | SRP061528 | PRJNA290839 | Danio rerio Transcriptome or Gene expression | PRJNA290839 | Transcriptome Analysis | RNA Seq of Danio rerio transcriptome | Polr1c2 | breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish Polr1c2|treatment:KO|BioSampleModel:Model organism or animal | RNA Seq of Polr1c2 | RNA Seq of Polr1c2 | 1 | Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina MiSeq | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP061528 | Polr1c2_S2_L001_R1_001.fastq.gz Polr1c2_S2_L001_R2_001.fastq.gz | bam fastq | 1024040592.0 | 3467167.0 | RNA Seq of Polr1c2 | 0:147.69 1:147.67 | A:280222262;C:231619577;G:229733851;T:282415559;N:49343 | 147 | 147 | 280222262 | 231619577 | 229733851 | 282415559 | 49343 | SRX1117105 | SRS1010315 | SRA279862 | The Chinese University of Hong Kong | The Chinese University of Hong Kong | 2 | 0.94843 | 0.95151 | 0.09589 | 0.09554 | 0.68747 | 0.68694 | 0.48798 | 0.48429 | 150 | 151 | B | B | biological fallback assumption | illumina | miseq | unknown | random_priming | trueseq | bulk | bulk | bulk | China | 2016-07-24 | Larval | Larval | Whole Organism | All anatomical structures |