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Skeletal and limb anomalies as a result of mutation in hnrnpul1 in zebrafish

ABSTRACT: Skeletal and limb anomalies as a result of mutation in hnrnpul1 in zebrafish

PROVIDER: PRJNA604782 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11016367_1.fastq.gz	Fastqsanger.gz
	SRR11016367_2.fastq.gz	Fastqsanger.gz
	SRR11016368_1.fastq.gz	Fastqsanger.gz
	SRR11016368_2.fastq.gz	Fastqsanger.gz
	SRR11016369_1.fastq.gz	Fastqsanger.gz

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Skeletal and limb anomalies as a result of mutation in hnrnpul1 in zebrafish

Project description:Mutations in RNA binding proteins can lead to pleiotropic phenotypes including craniofacial, skeletal, limb and neurological symptoms. Here, we show a developmental role for hnrnpul1 in the zebrafish limb, craniofacial development and in adult onset scoliosis. Furthermore, we demonstrate for the first time a role of hrnpul1 in alternative splicing regulation.

2020-02-05 | GSE144754 | GEO

Next Generation Sequencing of Wild Type and Hnrnpul1-/- RAW 264.7 Cells Transcriptomes

Project description:Purpose: The goal of this study is to compare NGS-derived wild type and Hnrnpul1 knockout (Hnrnpul1-/-) RAW 264.7 cells transcriptomes with or without LPS stimulation. Methods: Sequancing was performed by Novogene China Co. Ltd. RNA profiles of wild type and Hnrnpul1-/- RAW 264.7 cells as well as LPS stimulated (10 h) wild type and Hnrnpul1-/- RAW 264.7 cells were generated by deep sequencing using Illumina Novaseq 6000. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Method of TMM was used to normalize the readcount. Negative binomial distribution model was used to calculate the P value, and FDR was calculated by the method of Benjaminiand Hochberg. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (GRCm38/mm10). Comparing to wild type RAW 264.7 cells, 237 genes were up-regulated and 181 genes were down-regulated in Hnrnpul1-/- cells. At 10 h following LPS stimulation, 341 genes were up-regulated and 288 genes were down-regulated in Hnrnpul1-/- cells. Genes were pre-ranked according to log2FoldChange(KO/WT) followed by GSEA and 6 gene sets were significantly enriched. Significantly differential genes were undergone GO analysis (biological process) and biological process including cell-cell adhesion, positive regulation of cell activation and regulation of response to external stimulus were enriched. Conclusions: Lacking Hnrnpul1 promotes the expression of inflammatory cytokines in LPS stimulated RAW 264.7 cells.

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Wild Type and Hnrnpul1-/- RAW 264.7 Cells

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Project description:[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities. Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome. aCGH control vs. patient, total of 7 patients Lowest normalized log2 ratio = patient 1: -1.99; patient 2: -1.87; patient 3: -2.16; patient 4: -2.11; patient 5: -1.974802452; patient 6: -2.23; patient 7: -1.36.

2010-12-31 | E-GEOD-19932 | biostudies-arrayexpress

Recurrent 17q23.2 microdeletion flanked by segmental duplications associated with heart defects and limb abnormalities

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