run_metadata: 71860
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 71860 | SRR22135238 | SRX18114786 | SRS15617125 | SRP405741 | PRJNA896643 | Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils | GSE217064 | Transcriptome Analysis | Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet. | pubmed:37672586 | D Emergency granulopoiesis neutrophils post infection rep 4 | GSM6704384 | tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection | D Emergency granulopoiesis neutrophils post infection rep 4 | The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis | Neutrophil | At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella. | Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina. | Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C | cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection | GSM6704384 | GSM6704384: D Emergency granulopoiesis neutrophils post infection rep 4; Danio rerio; RNA Seq | GSM6704384 r1 | GSM6704384 | 1 | Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP405741 | loader:fastq load.py | D4_S16_L001_R1_001.fastq.gz | fastq | 492998897.0 | 6538726.0 | GSM6704384 r1 | 0:75.40 | A:142208659;C:103614806;G:105979666;T:141151718;N:44048 | 75 | 142208659 | 103614806 | 105979666 | 141151718 | 44048 | SRX18114786 | SRS15617125 | SRA1532054 | Hall, FMHS, University of Auckland | Hall, FMHS, University of Auckland | 1 | 0.90296 | 0.31723 | 0.76771 | 0.48693 | 75 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | nextera | sc | single_cell_plate | smartseq | New Zealand | 2022-11-01 | Larval | Larval | Blood | Hematopoietic System |