run_metadata: 76966

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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.				fbln rep3	GSM7658113		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 20–25 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.	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°C. 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°C 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP451003		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			2124108601	1805125896	1825004607	2143248362	351973	SRX21134297	SRS18399043	SRA1678716	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	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		Belgium	2023-07-24	Multi-stage	Multi-stage	Head	Nervous System