{"database": "metadata", "table": "run_metadata", "rows": [[33827, "SRR30712583", "SRX26116352", "SRS22679891", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt I 2", "GSM8523051", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing", "wt I 2", "fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:injured", "GSM8523051", "GSM8523051: wt I 2; Danio rerio; RNA Seq", "GSM8523051 r1", "GSM8523051", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525059_S24_R1_001.fastq.gz 1525059_S24_R2_001.fastq.gz", "fastq fastq", 8553382920.0, 28322460.0, "GSM8523051 r1", "0:151 1:151", "A:2189680208;C:2131369869;G:1994221174;T:2237623798;N:487871", 151, 151, null, null, 2189680208, 2131369869, 1994221174, 2237623798, 487871, "SRX26116352", "SRS22679891", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular 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": ["33827"], "units": {}, "query_ms": 8.831486004055478}