run_metadata: 38283
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 |
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| 38283 | SRR1611972 | SRX732526 | SRS721346 | SRP048902 | PRJNA263811 | Gene expression profiling of Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t zebrafish embryos at 3 dpf | GSE62273 | Transcriptome Analysis | We use next generation sequencing of embryos with neuronally expressed EWSR1 ERG at 3 dpf to investigate overlap between these embryos' regulated gene set and that of other Ewing sarcoma models Overall design: This deep sequence study was designed to determine the gene expression profile regulated by EWSR1 ERG. Samples were obtained at 3 days post fetilisation from Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999tRNA embryos expressing EWSR1 ERG neuronally or wild type siblings. RNA was isolated from 15 embryos per sample using the RNeasy Micro Kit Qiagen. | 6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG | GSM1524333 | tissue:Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf with neuronally expressed EWSR1 ERG|biological replica:1 | 6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG | GeneTiles was used for quantification and visualization of the RNAseq data Bowtie2 is used to align the reads in the fastq file to the genome obtained from Ensemble. Bowtie2 generates SAM files that contain the reads together with the location on the genome. Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome resulting in a sorted BAM file. The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file. Using the available annotation from Ensemble we can search the BAM file for reads within a gene using exon starting positions and lengths. This is done with a python script. The output of this script is a tab separated file tsv containing the read counts per gene. We used DESeq an R script to perform statistical analysis. The DESeq script is used to normalise the reads per gene based on divided by the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P value by calculating the dispersion per gene using DESeq. The size factors as well as the P values are stored in ‘tsv’ files. Using a script all tsv files are combined into tsv files e.g. per experiment chromosome per filtered results of most significant reads or highest ratio between measurement and control. Genome build: Zv9 toplevel | Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf | Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols | Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts. | genotype/variation:Embryos with neuronally expressed EWSR1 ERG|biological replica:1 | GSM1524333 | GSM1524333: 6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG; Danio rerio; RNA Seq | GSM1524333 | 1 | Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM1524333 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP048902 | 426266619.0 | 8358169.0 | GSM1524333 r1 | 0:51 | A:112004069;C:103380899;G:98829082;T:112000953;N:51616 | 51 | 112004069 | 103380899 | 98829082 | 112000953 | 51616 | SRX732526 | SRS721346 | SRA190781 | GEO | Leiden University, Institute of Biology Leiden | 1 | 0.93027 | 0.05803 | 0.69493 | 0.45892 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Netherlands | 2014-10-10 | Larval | Larval | Brain | Nervous System |