run_metadata: 24786
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 24786 | SRR25502050 | SRX21232928 | SRS18488022 | SRP453114 | PRJNA1001808 | The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger | GSE239949 | Transcriptome Analysis | From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries. | pubmed:28382966 | Sample 15 05316 MCK mut1 | GSM7678166 | tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing | Sample 15 05316 MCK mut1 | Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample | lyz+ mpx+ granulocytes | RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation. | cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf | GSM7678166 | GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq | GSM7678166 r1 | GSM7678166 | 1 | RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1500 | SRP453114 | 15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz | fastq fastq | 4459467180.0 | 21235558.0 | GSM7678166 r1 | 0:105 1:105 | A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798 | 105 | 105 | 1206908747 | 1012207561 | 1060393698 | 1179731376 | 225798 | SRX21232928 | SRS18488022 | SRA1685493 | Rural Clinical Sciences, La Trobe University | Rural Clinical Sciences, La Trobe University | 2 | 0.75719 | 0.88462 | 0.20719 | 0.24095 | 0.78559 | 0.77914 | 0.50538 | 0.55691 | 105 | 105 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Australia | 2023-08-03 | Hatching | Embryo | Blood | Hematopoietic System |