{"database": "metadata", "table": "run_metadata", "rows": [[76966, "SRR25396269", "SRX21134297", "SRS18399043", "SRP451003", "PRJNA997901", "Zebrafish fbln1 mutant ulg075 larvae at 10dpf versus AB wt", "GSE238059", "Transcriptome Analysis", "We generated a 16 nucleotide deletion mutant in the zebrafish fbln1 gene and we compared the whole larvae transcriptome to wt siblings in 10dpf larvae. Overall design: fbln1+/  parents were crossed  wt and fbln1 /  homozygous mutants were selected in three independant batches about 20 individuals/sample for extracting RNA and performing RNA Seq. Each mutant batch was compared to its wt siblings.", null, null, null, "fbln rep3", "GSM7658113", null, "source name:larvae heads|tissue:larvae heads|strain background:AB|genotype:ulg075|time point:10 dpf|geo loc name:missing|collection date:missing", "fbln rep3", "Approximatively 20\u201325 M reads were sequenced per sample. The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  Peltzer et al. 2020 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org; accessed 1 May 2020 Differential gene expression analysis was performed using the DESeq2 pipeline Love  Huber et al. 2014. Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Table counts fbln1/wt.csv containing individual counts: Ensembl gene Id  gene name fbln1 WT i R1 fbln1 WT ii R1 fbln1 WT iii R1 fbln1 mu i R1 fbln1 mu ii R1 fbln1 mu iii R1 Supplementary files format and content: Table fbln1/wt.csv containing:  Ensembl gene ID gene name log2FoldChange lfcSE stat pvalue padj Mu baseMean WT baseMean baseMean", "larvae heads", "Homozygous mutants were obtained by crossing heterozygous parents carrying the desired mutation. Resulting larvae were first sacrificed by exposure to MS 222 Ethyl 3 aminobenzoate methane sulfonate; Merck  Overijse  Belgium  10dpf larvae were stored in RNA later Fisher Scientific  Merelbeek  Belgium. Individual fish were decapitated  the heads anterior of each individual were stored in a 96 well plate for later RNA extraction  whereas the body posterior was used for DNA extraction and genotyping using q PCR. Once the genotypes were known  the heads were recovered and pooled to constitute wt and fbln1 /  batches of 21 individuals.", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer\u2019s instructions.", "Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28\u00b0C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28\u00b0C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf", "tissue:larvae heads|strain background:AB|genotype:ulg075|time point:10 dpf", "GSM7658113", "GSM7658113: fbln rep3; Danio rerio; RNA Seq", "GSM7658113 r1", "GSM7658113", "1", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451003", null, "loader:fastq load.py", "fbln1-mu-iii_NGS22-Y630_AH5MKYDSX5_S652_L002_R1_001.fastq.gz fbln1-mu-iii_NGS22-Y630_AH5MKYDSX5_S652_L002_R2_001.fastq.gz", "fastq fastq", 7897839439.0, 29176341.0, "GSM7658113 r1", "0:135.32 1:135.37", "A:2124108601;C:1805125896;G:1825004607;T:2143248362;N:351973", 135, 135, null, null, 2124108601, 1805125896, 1825004607, 2143248362, 351973, "SRX21134297", "SRS18399043", "SRA1678716", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", 2, 0.90473, 0.90217, 0.11614, 0.1131, 0.66959, 0.66996, 0.48247, 0.48066, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-07-24", "Multi-stage", "Multi-stage", "Head", "Nervous 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": ["76966"], "units": {}, "query_ms": 7.188155999756418}