run_metadata: 63839
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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| 63839 | SRR14077616 | SRX10451894 | SRS8583179 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | runx1 / kidney6 [runx1] | GSM5212433 | source name:adult kidney|genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | runx1 / kidney6 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212433 | GSM5212433: runx1 / kidney6 [runx1]; Danio rerio; RNA Seq | GSM5212433 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212433 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.4.8142704.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142704.2.cln.fq.gz | fastq fastq | 5830417310.0 | 23547116.0 | GSM5212433 r1 | 0:123.80 1:123.80 | A:1528065414;C:1374560308;G:1389503409;T:1538204560;N:83619 | 123 | 123 | 1528065414 | 1374560308 | 1389503409 | 1538204560 | 83619 | SRX10451894 | SRS8583179 | SRA1210911 | GEO | NHGRI | 2 | 0.94227 | 0.9443 | 0.0312 | 0.03106 | 0.7305 | 0.73198 | 0.4564 | 0.45229 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System |