{"database": "metadata", "table": "run_metadata", "rows": [[24854, "SRR25519420", "SRX21249697", "SRS18503946", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 4  3dpf", "GSM7681266", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681266", "GSM7681266: zebrafish  AR42 TFA 4  3dpf; Danio rerio; RNA Seq", "GSM7681266 r1", "GSM7681266", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_4.R1.fq.gz AR42_TFA_4.R2.fq.gz", "fastq fastq", 9896772900.0, 32989243.0, "GSM7681266 r1", "0:150 1:150", "A:2382403653;C:2457377213;G:2470646159;T:2586345875;N:0", 150, 150, null, null, 2382403653, 2457377213, 2470646159, 2586345875, 0, "SRX21249697", "SRS18503946", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70537, 0.88934, 0.03159, 0.04209, 0.78013, 0.75416, 0.50713, 0.45138, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "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": ["24854"], "units": {}, "query_ms": 14.695514997583814}