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IlApoCrat

ABSTRACT: Aporia crataegi (black veined white), genomic and transcriptomic data

PROVIDER: PRJEB45663 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	ERR6363320_1.fastq.gz	Fastqsanger.gz
	ERR6363320_2.fastq.gz	Fastqsanger.gz
	ERR6363321_1.fastq.gz	Fastqsanger.gz
	ERR6363321_2.fastq.gz	Fastqsanger.gz
	ERR6363316_1.fastq.gz	Fastqsanger.gz

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1 - 5 of 13

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ilApoCrat

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Affymetrix SNP array data for Dwarf and Rhode Island Red chicken samples

Project description:The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. We found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines.

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ilTriCrat

Project description:Trichiura crataegi (pale eggar), genomic and transcriptomic data

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Transcriptomic analysis of pancreatic adenocarcinoma specimens obtained from Black and White patients

Project description:In pancreatic cancer clinical trials, Black patients are under-represented while having higher morbidity and mortality rates as compared to other racial groups. Multiple factors, including socioeconomic and lifestyle factors may contribute to this disparity, but genomic contributions remain unclear. In an exploratory project to identify genes that may contribute to differences in survival between Black and White patients with pancreatic cancer, transcriptomic sequencing of over 24,900 genes was performed in human pancreatic tumor and non-tumor tissue obtained from Black and White patients. Over 4,400 genes were differentially expressed in tumor and non-tumor tissue, irrespective of race. Of these 4,400 genes, four (AGR2, POSTN, TFF1, and CP) met the pre-defined statistical threshold for upregulation in pancreatic tumor tissue; these findings were confirmed by quantitative PCR. Transcriptomic analysis of pancreatic tumor tissue in Black and White patients revealed differential expression in 1,200 genes. Non-tumor and tumor gene expression differences within each race were assessed, revealing over 1,500 tumor-specific differentially expressed genes in pancreatic tumor and non-tumor tissue from Black patients. We identified TSPAN8 as a potential tumor-specific gene significantly overexpressed in pancreatic tumor tissue in Black patients as compared to White patients. Using Ingenuity Pathway Analysis software to compare the race-associated gene expression profiles, over 40 canonical pathways were identified to be potentially impacted by the gene expression differences between the races. Heightened expression of TSPAN8 was associated with poor overall survival, suggesting TSPAN8 as one potential genetic factor contributing to the differential outcomes in Black patients with pancreatic cancer, supporting the potential utility of larger genomic studies to further explore the role of TSPAN8 in pancreatic cancer.

2023-01-19 | GSE211398 | GEO

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