run_metadata: 68839
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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| 68839 | SRR18210595 | SRX14357146 | SRS12170697 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3 / knockout rep5 | GSM5930978 | source name:30 zebrafish larvae|genotype/variation:elmo3|tissue:30 zebrafish larvae | elmo3 / knockout rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:elmo3|tissue:30 zebrafish larvae | GSM5930978 | GSM5930978: elmo3 / knockout rep5; Danio rerio; RNA Seq | GSM5930978 r1 | GSM5930978 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K3H_1.fq.gz K3H_2.fq.gz | fastq fastq | 4200293800.0 | 42002938.0 | GSM5930978 r1 | 0:100 1:100 | A:1111878794;C:972313858;G:1004784160;T:1111316988;N:0 | 100 | 100 | 1111878794 | 972313858 | 1004784160 | 1111316988 | 0 | SRX14357146 | SRS12170697 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95476 | 0.08651 | 0.67996 | 0.49703 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined |