run_metadata: 52867
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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| 52867 | SRR9320540 | SRX6088057 | SRS4989404 | SRP201776 | PRJNA549478 | Gene expression analysis of hematopoietic stem/progenitor cells in the zebrafish kidney | GSE132927 | Transcriptome Analysis | Hematopoietic stem cells HSCs maintain the entire blood system throughout the life and are utilized for a therapeutic component of blood diseases. The zebrafish is an elegant genetic model for the study of hematopoiesis due to its many unique advantages. We have developed the method to isolate zebrafish HSCs by a combination of two HSC related transgenic lines gata2a:GFP and runx1:mCherry. In this study we performed RNA seq analysis in three distinct hematopoietic cell populations in the adult kidney gata2a+ runx1+ cells HSCs gata2a runx1+ cells erythroid and/or myeloid primed progenitors and gata2a+ runx1 cells lymphoid primed progenitors. Overall design: mRNA profiles of isolated gata2a+ runx1+ cells gata2a runx1+ cells and gata2a+ runx1 cells in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500. | pubmed:31578390 | gata2a+ runx1 | GSM3896451 | source name:lymphoid primed progenitors|tissue:Sorted cells from the kidney|cell type:gata2a+ runx1 |age:adult|genotype:wild type | gata2a+ runx1 | Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. | lymphoid primed progenitors | Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina. | tissue:Sorted cells from the kidney|cell type:gata2a+ runx1 |age:adult|genotype:wild type | GSM3896451 | GSM3896451: gata2a+ runx1 ; Danio rerio; RNA Seq | GSM3896451 | 1 | Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP201776 | gata2a+_runx1-_R2.fastq.gz gata2a+_runx1-_R1.fastq.gz | fastq fastq | 3262502100.0 | 10875007.0 | GSM3896451 r1 | 0:150 1:150 | A:832656373;C:815169099;G:759749436;T:854690002;N:237190 | 150 | 150 | 832656373 | 815169099 | 759749436 | 854690002 | 237190 | SRX6088057 | SRS4989404 | SRA900579 | GEO | Kanazawa University | 2 | 0.92596 | 0.92513 | 0.0638 | 0.06526 | 0.77264 | 0.77644 | 0.47852 | 0.47703 | 150 | 150 | B | B | biological fallback assumption | illumina | nextseq | 3prime | poly_a | nextera | sc | single_cell_plate | quartzseq | Japan | 2019-06-18 | Adult | Adult | Kidney | Renal System |