run_metadata: 64994

This data as json

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64994	SRR14883464	SRX11200544	SRS9255523	SRP325167	PRJNA740056	Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.	GSE178709	Transcriptome Analysis	The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a / zebrafish model we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids with disruption to cell cycle modulation and epigenetic transcriptional control. Hence using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation identifying hypermethylated pathways involving biological adhesion Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS confirming cell cycle involvement and disturbance of TGFbeta BMP Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a / and control wildtype. Biological replicates were taken.		pubmed:36656098		wildtype retina rep 2 [R56 WT02]	GSM5396385		source name:wildtype retina\|genotype:wildtype A/B\|hpf:56\|tissue:dorsal retina	wildtype retina rep 2 [R56 WT02]	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample	wildtype retina		RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input kit using standard protocols	zebrafish were harvested at appropriate time points hpf retinal regions dissected	genotype:wildtype A/B\|hpf:56\|tissue:dorsal retina	GSM5396385	GSM5396385: wildtype retina rep 2 [R56 WT02]; Danio rerio; RNA Seq	GSM5396385		1	RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input kit using standard protocols	GEO Accession:GSM5396385	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP325167			R56-WT02_R1.fastq.gz R56-WT02_R2.fastq.gz	fastq fastq	2736567000.0	13682835.0	GSM5396385 r1	0:100 1:100	A:774624618;C:594658601;G:615415962;T:749131027;N:2736792	100	100			774624618	594658601	615415962	749131027	2736792	SRX11200544	SRS9255523	SRA1249569	GEO	Institute of Ophthalmology, UCL	2	0.93365	0.93451	0.17399	0.17557	0.74237	0.74483	0.51877	0.50425	100	100	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown		United Kingdom	2021-06-22	Undetermined	Undetermined	Eye	Sensory System