Transcriptome profiles reveals potential core genes in the black skin of Xichuan Black-bone chickens（Gallus gallus）
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE128028 | GEO | 2019/06/21
REPOSITORIES: GEO
Similar Datasets
Project description:Relative expression levels of mRNAs in chicken cecal epithelia experimentally infected with Eimeria tenella were measured at 4.5 days post-infection. Two weeks old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of Eimeria tenella. Cecal epithelia samples were collected from >12 birds in infected or uninfected group at 4.5 d following infections, in which samples from 4 birds were pooled together to form a total 3 biological replicates in each group. Parasite merozoites were also collected from four infected chickens at 5 d after infections. Uninfected control samples, merozoites and infection group samples were selected for RNA extraction and hybridization on Affymetrix microarrays. We used Affymetrix GeneChip chicken genome arrays to detail the chicken cecal epithelia gene expression in the control and E. tenella-infected birds.
2012-12-10 | GSE39602 | GEO
Project description:High throughput sequencing technology was used to sequence the transcriptome of breast muscle tissue of Test II group and test group IV
2021-02-01 | GSE127058 | GEO
Project description:Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease (CHD). Amniotic fluid (AF) contains a higher abundance of biological compounds which could direct reflect the information of fetal health. AF-derived exosomal miRNAs have been investigated as etiological factors in the pathogenesis of TOF. The purpose of this study was to analyze the expression of AF-derived exosomal miRNAs and their roles in TOF development. In this study, we identified differentially expressed (DE)-miRNAs between TOF group and control group. A total of 257 miRNAs were differentially expressed (DE) between TOF and control groups. KEGG pathway enrichment demonstrated that these target genes of DE-miRNAs were involved in Wnt and Notch signaling pathway. Twenty five of 257 DE-miRNAs were overlapped with Notch-regulated and Wnt-regulated miRNAs simultaneously.
2021-10-19 | GSE186059 | GEO
Project description:In this study, we sequenced the complete mitochondrial genome (mitogenome) of the Huangshan Black chicken (HBC). Results showed that the complete HBC mitogenome was 16,785 bp in size, comprising 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and 1 non-coding control region (D-loop). The overall nucleotide composition was 32.5% for C, 30.3% for A, 23.7% for T, and 13.5% for G. Phylogenetic analysis showed that the HBC mitogenome was clustered with Xianju chicken, which belonged to the haplogroup D2. Our results therefore demonstrate that the origin of HBC corresponds to haplogroup D2 distribution and might have at least one maternal lineage originated from Southeast Asia.
| S-EPMC7872527 | biostudies-literature
Project description:The black-bone chicken (Gallus gallus domesticus) is a breed of chicken that is commonly found in Thailand. This breed is known for having a number of black colored organs. Consumers have been notably attracted to the black-bone chicken breed for the characteristic darkness that is observed in many of its organs. However, the degree of darkness in all organs of the black-bone chicken is still in question. Importantly, there have not yet been any published reports on the distribution of melanin pigment in the organs of the black-bone chicken. This research study aims to examine the distribution of the melanin pigment in 33 organs of the Thai black-bone chicken. Ten black-bone chickens (five male, five female) were included in this study. Thirty-two organs including the brain, spinal cord, sciatic nerve, larynx, trachea, syrinx, lungs, heart, pericardium, aorta, brachial vein, kidney, cloaca, oviduct, testis, gastrocnemius muscle, femur, tongue, esophagus, crop, proventriculus, gizzard, duodenum, jejunum, ileum, cecum, pancreas, liver, gall bladder, omentum, abdominal fat, spleen, and skin were examined in this study. Histological sections taken from tissue samples of each of these organs were studied. The findings revealed that the presence of the melanin pigment was not significantly different (p > 0.005) between male and female specimens. Notably, the liver was the only organ in which the melanin pigment had not accumulated. Consequently, there was not a uniform pattern of melanin pigment accumulation throughout the organs of the chickens. The melanin pigment was present in all of the tissue layers of most organs, while the melanin pigment was found in only specific layers of some of the organs. In conclusion, the distribution of melanin pigmentation in the organs of each of the animals in this study was found to be different. However, in some tissue samples, such as those obtained from the liver, no accumulation of the melanin pigment was observed.
| S-EPMC7278803 | biostudies-literature
Project description:Black-bone chickens (Gallus gallus domesticus) have become economically valuable, particularly in Southeast Asia as a consequence of popular traditional Chinese medical practices. Chickens with whole body organ darkness are considered to have higher value and are, therefore, more often requested. This research study aimed to investigate the darkness in 34 skeletal muscles of 10 Thai black-bone chickens (five males and five females). The evaluation of muscle darkness was done on two levels: (i) a color chart was employed at the macroanatomical level and (ii) by using melanin pigment to evaluate the structure at the microanatomy level. The results revealed that the accumulation of melanin pigment in the muscle tissue was observed in the endomysium, perimysium and epimysium. With respect to the results of the color chart test, iliotibialis lateralis pars preacetabularis, gastrocnemius, fibularis longus and puboischiofemoralis pars medialis showed the highest degree of darkness, while serratus profundus, pectoralis, iliotibialis cranialis, flexor cruris lateralis, and flexor cruris medialis appeared to be the least dark. In addition, we found that the highest and lowest amounts of melanin pigment was noted in the flexor carpi ulnaris and pectoralis (p < 0.05), respectively; however, there was no significant difference (p > 0.05) observed between the sexes. These results reveal that the 34 specified muscles of black-bone chickens showed uneven distribution of darkness due to the differing accumulations of melanin pigments of each muscle.This information may provide background knowledge for a better understanding of melanin accumulation and lead to breeding improvements in Thai black-bone chickens.
| S-EPMC7811297 | biostudies-literature
Project description:Relative expression levels of mRNAs in chicken cecal epithelia experimentally infected with Eimeria tenella were measured at 4.5 days post-infection. Two weeks old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of Eimeria tenella. Cecal epithelia samples were collected from >12 birds in infected or uninfected group at 4.5 d following infections, in which samples from 4 birds were pooled together to form a total 3 biological replicates in each group. Parasite merozoites were also collected from four infected chickens at 5 d after infections. Uninfected control samples, merozoites and infection group samples were selected for RNA extraction and hybridization on Affymetrix microarrays. We used Affymetrix GeneChip chicken genome arrays to detail the chicken cecal epithelia gene expression in the control and E. tenella-infected birds. Infected, uninfected chicken cecal epithelia and merozoites were selected for RNA extraction and hybridization with Affymetrix microarrays. Our goal was to analyze global transcriptome changes in chicken cecal mucous membranes in response to E. tenella infection in vivo. We used infected (T1,T2,T3; three biological replicates) and uninfected (Neg1, Neg2, Neg3; three biological replicates) samples to identify genes that were differentially expressed. Meanwhile, RNA and probes were also prepared from parasite merozoites (Mzt) from infected samples (Mzt) and used as an additional control in microarray hybridization.
2012-12-10 | E-GEOD-39602 | biostudies-arrayexpress
Project description:In this study, the complete mitochondrial genome of Emei black chicken (Gallus gallus) was obtained by using next generation sequencing method. The complete mitogenome sequence is 16,784 bp in length, containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and one control region. This work provides a valuable genetic resource of data for the Gallus gallus evolution study and contributes to the breeding improvement program of native chicken breeds.
| S-EPMC7781979 | biostudies-literature
Project description:Psoraleae Fructus can cause liver damage, we study its effect on liver transcription,According to the sequence data, a total 6689 mRNAs were identified. Compared with control group, 1814 differential mRNAs were identified in the SPHD group, including 939 upregulated mRNAs and 875 downregulated mRNAs. Top 20 pathways are shown in the result, including “Metabolic pathways”, “NOD−like receptor signaling pathway”, “PI3K−Akt signaling pathway”, “Drug metabolism − other enzymes”, and “Estrogen signaling pathway”. To understand the functions of differential mRNAs, the target genes of differential mRNAs were predicted and were mapped to terms in the GO database and compared with the background (Figure 5C). The GO has 3 ontologies, which are “biological process”, “cellular component”, and “molecular function”. In the “biological process” part, most genes were related to “immune system process”, “oxidation−reduction process”, and “transport”. In the “cellular component” part, most genes were related to the “ribosomal part”, “mitochondrial part” and “membrane part”. In the “molecular function” part, most genes were related with “structural constituent of ribosome part”, “protein binding ” and “poly(A) RNA binding”.
2024-09-29 | GSE185007 | GEO
Project description:RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens
| PRJNA247105 | ENA