Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Skin transcriptome profiles associated with black- and white-coated region in a crossbred goat

ABSTRACT: we compared the skin transcriptomes of the black- and white-coated region from the Boer and Macheng Black crossbred goat with black head and white body using the Illumina RNA-Seq method. Six cDNA libraries derived from skin samples of the white coat region (n = 3) and black coat region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for each skin sample of black coat and white coat, respectively, of which 75.39% and 76.05% reads were covered in the genome database. Our study provides insight into the transcriptional regulation of two distinct coat color that might serve as a key resource for understanding coat color pigmentation of goat.

ORGANISM(S): Capra hircus

PROVIDER: GSE135963 | GEO | 2022/08/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Whole-transcript Expression data from skin of different coat color in Chinese Merion (Junken type)

Project description:Coat color mainly reflects pigmentation resulting from melanin. Wool color is one of the most visible and heritable traits in sheep. Although several detailed molecular mechanisms involved in coat color have been elucidated, our understanding of differences in gene expression patterns of wool color-related genes in Chinese Merino (Junken type) is limited. We employed the Affymetrix microarray to identify differentially expressed genes. 122 genes were differentially expressed, consisting of 117 upregulated and 5 downregulated genes that were related to black/brown skin. The expression level of the BMP2, BMP4, TYRP1, LEPR, DCT, BMPR1A, and TP45A genes was validated by qRT-PCR, and the results coincided with those of microarray. The expression level of ASIP in the black/brown group was significantly lower than that of the white group, suggesting that this plays a key role in the regulation of wool pigmentation. Some cloned color genes (MITF, MC1R, GPR143, and KIT) showed no significant differences in expression levels between the black/brown- and white-skinned sheep. Functional annotation by using Gene Ontology (GO) showed that the differentially expressed genes enriched specific GO terms, particularly those relating to melanin biosynthesis and metabolic processes. KEGG pathway analysis indicated that the categories of tyrosine metabolism and melanogenesis pathway were enriched with differentially expressed genes. Taken together, the present study has shown that the tyrosine metabolism pathway plays an essential role in regulating wool color. The findings of this study may also be utilized in the elucidation of the molecular mechanisms and relationship between genes and wool color in Chinese Merino (Junken type). We used microarrays to detail the global programme of gene expression and identified distinct different expression genes of skin in different coat color Chinese Merino (Junken type).

2018-04-01 | GSE98180 | GEO

Skin transcriptome profiles associated with black- and white-coated region in a crossbred goat

Project description:Skin transcriptome profiles associated with black- and white-coated region in a crossbred goat

| PRJNA560789 | ENA

Cyprinus carpio 'koi' Raw sequence reads

Project description:Genome-wide analysis of skin color-related lncRNA and mRNA expression in Koi carp, Cyprinus carpio L. LncRNAs information linked to fish skin color regulation is over-limited. In this study, Illumina sequencing and bioinformatics were primarily conducted on black, white and red skin colors of Koi carp. A total of 590,415,050 clean reads, 446,614 putative transcripts, 4,252 known and 72,907 novel lncRNAs were simultaneously obtained, respectively. Out of these genes, 92 significant differentially expressed lncRNAs and 722 mRNAs were excavated. Ccr_lnc5622441, Ccr_lnc765201 were found up-regulated in black and red skins; Ccr_lnc14074601 were up-regulated in white skin; and premelanosome proteins a (Pmela), tyrosinase (Tyr) were up-regulated in black skin, etc. Quantitative real-time PCR (qRT-PCR) further validated 12 differentially expressed genes were consistent with RNA-seq. Moreover, 70 lncRNAs on 107 target mRNAs in cis and 79 lncRNAs on 41,625 target mRNAs in trans were investigated, the networks revealed one lncRNAs can connected with numerous mRNAs, vice versa. These findings broadened the lncRNAs landscape of skin colors and provided new insights into the mechanisms underlying lncRNAs mediated pigmentation and differentiation in Koi carp.

2019-01-15 | GSE125039 | GEO

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.

2019-05-02 | GSE130568 | GEO

Skin transcriptome profiles associated with skin color in chickens

Project description:This work was to study the transcriptome profiles in the skin of chickens with black versus white skin using high-throughput RNA deep-sequencing technology, to investigate the different expression profiles of the genes involved in skin pigmentation, then look for the main differences between black and white skin colors in Lueyang chickens. 16-week-old white and black female Lueyang chickens (5 birds per color) were selected for the sample collection. A piece of skin (8 mm in diameter) from the left back was collected . Total RNA was extracted from the sample using Trizol reagent . Three RNA samples from either the black or white skin samples were pooled following mRNA isolation. The sequencing of the library was performed using an Illumina HiSeq 2000 (LianChuan Sciences, Hangzhou, China). According the result of sequencing, some colored gene expressions were validated using Real time quantitative polymerase chain reaction (qPCR).

2015-05-20 | E-GEOD-68460 | biostudies-arrayexpress

Bovine nose tissues: Yellow nose vs. Black nose

Project description:The coat color of mammals is determined by the melanogenesis pathway, which is responsible for maintaining the balance between black-brown eumelanin and yellow-reddish phaeomelanin. It is also believed that the color of the bovine nose is regulated in a similar manner; however, the molecular mechanism underlying pigment deposition in the black nose has yet to be elucidated. The aim of the present study was to identify melanogenesis-associated genes that are differentially expressed in the black vs. yellow nose of native Korean cows.

2013-12-26 | GSE53657 | GEO

Skin transcriptome profiles associated with skin color in chickens

2015-05-20 | GSE68460 | GEO

Bovine nose tissues: Yellow nose vs. Black nose

2013-12-26 | E-GEOD-53657 | biostudies-arrayexpress

Ogye body map RRBS data

Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).

2018-06-21 | GSE104355 | GEO

Ogye body map RNA-seq data

2018-06-21 | GSE104351 | GEO