{"database": "metadata", "table": "run_metadata", "rows": [[63533, "SRR13938391", "SRX10317715", "SRS8438152", "SRP310259", "PRJNA713782", "TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling", "GSE168727", "Transcriptome Analysis", "Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14  the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype  identifying imiquimod  an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation  the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/  or wildtype zebrafish embryos  which were phenylhydrazine Phz stressed or unstressed  and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.", null, null, null, "WT Phz DMSO 2", "GSM5160073", null, "tissue:TgItga2b:GFPlo cells|genotype:Rps14+/+|stress:Phz|treatment:DMSO", "WT Phz DMSO 2", "Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample", "TgItga2b:GFPlo cells", "Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 \u00b5g/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 \u00b5M Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.", "Embryos were pooled by rps14 genotype  stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol", "Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines", "genotype:Rps14+/+|stress:Phz|treatment:DMSO", "GSM5160073", "GSM5160073: WT Phz DMSO 2; Danio rerio; RNA Seq", "GSM5160073", null, "1", "Embryos were pooled by rps14 genotype  stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol", "GEO Accession:GSM5160073", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP310259", null, "loader:fastq load.py", "30_S30_L002_R1_001.fastq 30_S30_L002_R2_001.fastq", "fastq fastq", 633338417.0, 5230945.0, "GSM5160073 r2", "0:60.54 1:60.54", "A:172735379;C:141923833;G:147363448;T:171289741;N:26016", 60, 60, null, null, 172735379, 141923833, 147363448, 171289741, 26016, "SRX10317715", "SRS8438152", "SRA1205468", "GEO", "Department of Haematology, UCL Cancer Institute", 2, 0.91597, 0.92125, 0.17871, 0.18016, 0.75913, 0.7625, 0.54109, 0.54348, 61, 60, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2021-03-11", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["63533"], "units": {}, "query_ms": 8.052072997088544}