The chicken immature erythrocyte transcriptome
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE75848 | GEO | 2016/01/01
SECONDARY ACCESSION(S): PRJNA305527
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we identified and mapped out all the transcriptionally active chromosomal domains in the chicken immature erythrocyte genome, including the known β- and α-globin domains, by combining a powerful chromatin fractionation method with next generation DNA and RNA sequencing. Two biological replicates of total RNA were sequenced to characterize genes in chicken erythrocyte cells
2016-07-03 | E-GEOD-75848 | biostudies-arrayexpress
Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we identified and mapped out all the transcriptionally active chromosomal domains in the chicken immature erythrocyte genome, including the known β- and α-globin domains, by combining a powerful chromatin fractionation method with next generation DNA and RNA sequencing.
2016-01-01 | GSE75849 | GEO
Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we identified and mapped out all the transcriptionally active chromosomal domains in the chicken immature erythrocyte genome, including the known β- and α-globin domains, by combining a powerful chromatin fractionation method with next generation DNA and RNA sequencing. To characterize transcriptionally active chromatin domains, we used two biological replicates. Each replicate set has one control SE fraction and one transcriptionally active chromatin fraction (F1)
2016-07-03 | E-GEOD-75849 | biostudies-arrayexpress
Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that highly expressed genes were associated with H3K4me3 and H3K27ac.Our data provide a genome-wide profile of chromatin signatures in relation to expression levels in chicken immature erythrocytes. Examination of two different histone modifications in immature erythrocyte cells
2016-07-03 | E-GEOD-75845 | biostudies-arrayexpress
Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that highly expressed genes were associated with H3K4me3 and H3K27ac.Our data provide a genome-wide profile of chromatin signatures in relation to expression levels in chicken immature erythrocytes.
2016-01-01 | GSE75845 | GEO
Project description:The chicken erythrocyte epigenome
| PRJNA305808 | ENA
Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that immune genes were associated with H3K4me3 and H3K27ac.Our data provide a genome-wide profile of chromatin signatures for immune genes in chicken polychromatic erythrocytes.
2020-12-31 | GSE128864 | GEO
Project description:The genetic closeness and divergent muscle growth rates of broilers and layers make them great models for myogenesis study. In order to discover the molecular mechanisms determining the divergent muscle growth rates and muscle fiber sizes in different chicken lines, we systematically identified differentially expressed genes between broilers and layers during muscle development (postnatal 1 day, 2 weeks, 4 weeks, 6 weeks and 8 weeks) by microarray hybridization experiment. Taken together, 543 differentially expressed probe sets were found between broilers and layers across different developmental stages, including genes related to muscle growth and hypertrophy, fatty acid transportation and metabolism, protein degradation, and several important signaling pathways. The expression profiles of a few differentially expressed genes were highly correlated with the growth rates of broilers and layers. We also identified SNPs within upstream transcription factor binding sites of a few differentially expressed genes, indicating that these SNPs might be the causing factor of the expression differences of these genes between broilers and layers. These studies provided new clues for deciphering mechanisms underlining muscle development and organ size control in different chicken lines, will shed light on the study of human muscle related disease as well. Experiment Overall Design: Pectoralis major muscles were sampled from broilers and layers at indicated developmental stage (postnatal 1 day, 2 weeks, 4 weeks, 6 weeks and 8 weeks). Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. Affymetrix Gene Chip array hybridization was carried out according to Affymetrix Expression Analysis Technical Manual by GeneTech Biotechnology Limited Company (Shanghai, China). Following labeled cRNA fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45â on Affymetrix Chicken Genome Array. After standard washing and staining, GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
2009-01-14 | E-GEOD-9251 | biostudies-arrayexpress
Project description:This collection contains microRNA expression profiling data for samples purified from umbilical cord blood, belonging to one of the followiing populations: MEP, MEGA1, MEGA2, ERY1, ERY2, ERY3. MEP: megakaryocyte-erythrocyte precursors (defined by CD34+ CD38+ IL-3Ra- CD45RA- ); MEGA1: megakaryocyte population 1 (defined by CD34+ CD61+ CD41+ CD45- ); MEGA2: megakaryocyte population 2 (defined by CD34- CD61+ CD41+ CD45- ); ERY1: erythrocyte population 1 (defined by CD34+ CD71+ GlyA- ); ERY2: erythrocyte population 2 (defined by CD34- CD71+ GlyA- ); ERY3: erythrocyte population 3 (defined by CD34- CD71+ GlyA+ ). Keywords: microRNA, miRNA, MEP, megakaryocyte, erythrocyte, lineage specification
2008-06-10 | GSE10593 | GEO
Project description:Diamond Blackfan Anemia (DBA) is a rare, congenital erythrocyte aplasia that is usually caused by haploinsufficiency of ribosomal proteins due to diverse mutations in one of several ribosomal protein genes. A striking feature of this disease is that a range of different mutations in ribosomal proteins results in similar disease phenotypes primarily characterized by erythrocyte abnormalities and macrocytic anemia, while most other cell types are minimally affected. Previously, we analyzed the erythrocyte membrane proteomes of several DBA patients and identified several proteins that are not typically associated with this cell type that suggested inflammatory mechanisms contribute to the pathogenesis of DBA. In this study, we evaluated the erythrocyte cytosolic proteome of DBA patients through in-depth analysis of hemoglobin-depleted erythrocyte cytosol. The simple, reproducible, hemoglobin depletion using nickel columns enabled in-depth analysis of over 1000 cytosolic erythrocyte proteins with minimal subsequent fractionation of the proteome. Label-free quantitation and statistical analysis identified 29 proteins that were significantly changed in DBA patients compared to matched healthy control donors. Some of the proteins that were significantly increased in DBA erythrocyte cytoplasm included three proteasome subunit beta proteins that make up the immunoproteasome and proteins induced by interferon-γ such as n-myc interactor and interferon-induced 25 kDa protein [NMI and IFI35 respectively]. Pathway analysis confirmed the presence of an inflammatory signature with erythrocytes of DBA patients and predicted key upstream regulators including mitogen activated kinase 1, interferon-γ, tumor suppressor p53, and tumor necrosis factor. These results show that erythrocytes in DBA patients are intrinsically different from those in healthy controls which may be due to an inflammatory response resulting from the inherent molecular defect of ribosomal protein haploinsufficiency or changes in the bone marrow microenvironment that leads to red cell aplasia in DBA patients.
2018-10-24 | PXD002339 | Pride