run_metadata: 39914
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 39914 | SRR2255627 | SRX1187762 | SRS1056692 | SRP063370 | PRJNA294819 | Danio rerio PFOS FL transcriptome project | PRJNA294819 | Other | PFOS1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS1|BioSampleModel:Model organism or animal | PFOS1 | PFOS1 | PFOS1 | cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina MiSeq | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP063370 | PFOS1_S3_L001_R1_001.fastq.gz PFOS1_S3_L001_R2_001.fastq.gz | fastq fastq | 791950817.0 | 5244084.0 | PFOS1 | 0:75.53 1:75.48 | A:207476025;C:187690975;G:185784999;T:210781701;N:217117 | 75 | 75 | 207476025 | 187690975 | 185784999 | 210781701 | 217117 | SRX1187762 | SRS1056692 | SRA295687 | The Chinese University of Hong Kong | The Chinese University of Hong Kong | 2 | 0.96195 | 0.96213 | 0.051 | 0.04857 | 0.7386 | 0.73927 | 0.49669 | 0.49151 | 76 | 53 | B | B | biological fallback assumption | illumina | miseq | unknown | random_priming | trueseq | bulk | unknown | unknown | China | 2016-09-05 | Larval | Larval | Embryo Imprecise | All anatomical structures |