{"database": "metadata", "table": "run_metadata", "rows": [[36193, "SRR33446960", "SRX28687222", "SRS24954078", "SRP583344", "PRJNA1259437", "Inhibition of TGF beta signalling during zebrafish larval tail regeneration.", "GSE296469", "Transcriptome Analysis", "This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent  injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples  the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.", null, null, null, "DMSO treated / cut tail replicate 1", "GSM8970914", null, "source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing", "DMSO treated / cut tail replicate 1", "demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file", "Larval tail", "SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.", "100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit", "Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40\u2009\u03bcg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference", "tissue:Larval tail|genotype:Wild type|treatment:Tail excision", "GSM8970914", "GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq", "GSM8970914 r1", "GSM8970914", "1", "100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP583344", null, null, "Orange-1_S19_L003_R1_001.fastq.gz", "fastq", 355553156.0, 4678331.0, "GSM8970914 r3", "0:76", "A:101770613;C:75287760;G:78157774;T:100334741;N:2268", 76, null, null, null, 101770613, 75287760, 78157774, 100334741, 2268, "SRX28687222", "SRS24954078", "SRA2124571", "University of Sheffield", "University of Sheffield", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2025-05-06", "Larval", "Larval", "Tail", "Multi-system"]], "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": ["36193"], "units": {}, "query_ms": 9.751987003255635}