run_metadata: 60918
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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| 60918 | SRR12658662 | SRX9139720 | SRS7381386 | SRP282671 | PRJNA663959 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development | GSE158098 | Transcriptome Analysis | Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate n= 3 for each genotype. | parent bioproject:PRJNA663961 | pubmed:34492681 | runx1 / kidney1 | GSM4792205 | source name:adult kidney|strain:EK|genotype/variation:runx1 / del25 hg97|age:2.5 month|tissue:kidney | runx1 / kidney1 | RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM 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: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix. | adult kidney | RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2. | strain:EK|genotype/variation:runx1 / del25 hg97|age:2.5 month|tissue:kidney | GSM4792205 | GSM4792205: runx1 / kidney1; Danio rerio; RNA Seq | GSM4792205 | 1 | RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2. | GEO Accession:GSM4792205 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP282671 | runx1_del25_null_4.1.cln.fq.gz runx1_del25_null_4.2.cln.fq.gz | fastq fastq | 6973886556.0 | 27674153.0 | GSM4792205 r1 | 0:126 1:126 | A:1932833306;C:1502732434;G:1534451974;T:2003868842;N:0 | 126 | 126 | 1932833306 | 1502732434 | 1534451974 | 2003868842 | 0 | SRX9139720 | SRS7381386 | SRA1126725 | GEO | NHGRI | 2 | 0.93692 | 0.93786 | 0.11567 | 0.11588 | 0.74123 | 0.74099 | 0.56167 | 0.56297 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2020-09-16 | Juvenile | Juvenile | Kidney | Renal System |