run_metadata: 43252
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 43252 | SRR5921025 | SRX3081852 | SRS2420478 | SRP115124 | PRJNA397736 | Sequencing of Danio rerio skin from wildtype and two tert mutant phenotypes JenAge | GSE102434 | Transcriptome Analysis | Comparison of gene expression profiles from Danio rerio skin of wiltype AB and homozygous/heterozygous tert mutant phenotypes AB tert / AB tert+/. The RNA seq data comprises 3 groups. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: Overall Design: 13 samples in 3 groups: AB 5 samples AB tert / 3 samples AB tert+/ 5 samples | pubmed:34680427 | NH FLI 257 skin RNAseq | GSM2736508 | source name:skin|strain:AB wildtype|tissue:skin|age:3 month|Sex:male | NH FLI 257 skin RNAseq | Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10 and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample. | skin | Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction. | strain:AB wildtype|tissue:skin|age:3 month|Sex:male | GSM2736508 | GSM2736508: NH FLI 257 skin RNAseq; Danio rerio; RNA Seq | GSM2736508 | 1 | Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction. | GEO Accession:GSM2736508 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP115124 | 1149170556.0 | 22532756.0 | GSM2736508 r1 | 0:51 | A:322046038;C:255088738;G:249324620;T:322618409;N:92751 | 51 | 322046038 | 255088738 | 249324620 | 322618409 | 92751 | SRX3081852 | SRS2420478 | SRA597914 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.94133 | 0.06843 | 0.75917 | 0.66656 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2017-08-09 | Adult | Adult | Skin | Surface Structure |