run_metadata: 33827

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
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.				wt I 2	GSM8523051		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 µl 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 ◦C.	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 µl 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP533374			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			2189680208	2131369869	1994221174	2237623798	487871	SRX26116352	SRS22679891	SRA2089519	Institute of Molecular Genetic and Genetic Engineering	Institute of Molecular Genetic and Genetic Engineering												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		Serbia	2024-09-18	Adult	Adult	Muscle	Muscular System