{"database": "metadata", "table": "run_metadata", "rows": [[75332, "SRR24471192", "SRX20257903", "SRS17589514", "SRP436517", "PRJNA970301", "Bulk RNA seq analysis during fin regeneration of regeneration associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes", "GSE231956", "Transcriptome Analysis", "Bulk RNA seq analysis during fin regeneration of regeneration associated silencer s1 knockout zebrafish identified several up regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points 0  1 and 4 dy post amputation dpa  indicating that s1 has repressive ability to control downregulation of the nearby genes. Overall design: 10 caudal fins each of regeneration associated silencer s1 knockout zebrafish and their WT siblings at 0  1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.", null, "pubmed:38290519", null, "s1 KO fin 0dpa.rep3", "GSM7306449", null, "source name:caudal fin|tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa|geo loc name:missing|collection date:missing", "s1 KO fin 0dpa.rep3", "RNA seq reads were trimmed by Trim Galore v 0.6.7  with cutadapt v 3.5 and mapped with STAR v 2.7.10  with parameters   twopassMode Basic and supplying the Ensembl danRer11 annotation to zebrafish genome danRer11. The mapped reads were counted using R/Bioconductor GenomicAlignments packagev 1.30.0. Assembly: danRer11 Supplementary files format and content: tab delimited text files include normalized counts  for each Sample by library size", "caudal fin", "Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water.", "Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.", "Zebrafish of the outbred Ekkwill EK strain at about 4 month 8 month of age and regeneration associated silencer s1 knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily  and the water temperature was maintained at 27.5 \u00b0C and fish were kept on a 14/10 light/dark cycle.", "tissue:caudal fin|genotype:s1 silencer homozygous knockout|time:0dpa", "GSM7306449", "GSM7306449: s1 KO fin 0dpa.rep3; Danio rerio; RNA Seq", "GSM7306449 r1", "GSM7306449", "1", "Fins were amputated at 50% of their original length using scalpel Sterile Scalpel Blades #22  Feather. Biological triplicate pools of caudal fin clips from regeneration associated silencer s1 knockout fish and their WT siblings were collected at 0 dpa freshly amputated  1 dpa  or 4 dpa time points via scalpel Sterile Scalpel Blades #22  Feather from 10 fish per pool. Fin tissues were homogenized in Tri reagent Sigma and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit 5 Zymo. cDNA was synthesized from 20 ng of total RNA with a Maxima H minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel cutting and extraction  and 300   800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ MGI2000  100 bp PE  by BGI Americas.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP436517", null, null, "21_s1_KO_fin_0_dpa_L2_1.fq.gz 21_s1_KO_fin_0_dpa_L2_2.fq.gz", "fastq fastq", 5003838000.0, 25019190.0, "GSM7306449 r2", "0:100 1:100", "A:1274691496;C:1243030235;G:1160163118;T:1325934412;N:18739", 100, 100, null, null, 1274691496, 1243030235, 1160163118, 1325934412, 18739, "SRX20257903", "SRS17589514", "SRA1634637", "Poss, Cell Biology, Duke University", "Poss, Cell Biology, Duke University", 2, 0.84422, 0.87469, 0.14858, 0.15129, 0.79896, 0.79606, 0.58866, 0.6067, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-05-08", "Adult", "Adult", "Fin", "Surface Structure"]], "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": ["75332"], "units": {}, "query_ms": 13.458982997690327}