Mapping of low-salt soluble chromatin identifies known and novel transcriptionally active genes in chicken erythrocytes
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ABSTRACT:
PROVIDER: PRJNA486785 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7721759_1.fastq.gz | Fastqsanger.gz | |||
| SRR7721759_2.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional regulation is regulated by the organization of the genome into chromatin compartments and domains. Here, we present the detailed characteristics, including location of nucleosome-free regions, of several novel transcriptionally active/poised chromatin compartments exhibiting a range of transcriptional activities. These chromatin patterns illustrate how the salt solubility profile of a genomic region aids in the annotation of genes expressed in erythroid cells and contributes to the identification of functional features such as regulatory regions.
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Project description:Erythrocytes represent the most abundant cell type of the bloodstream in all vertebrates. The principal feature that differenciates erythrocytes of non-mammals is that unlike mammals they mantain the nucleus in their terminal differentiation. While the main function associated to erythrocytes is the oxygen and carbon dioxide transport, some other functions, no less important, have been attributed to these cells. The focus of this study was to investigate the response of cultured chicken erythrocytes to bacterial lipopolysaccharide (LPS), bacterial peptidoglycan (PGN) and to the analog viral dsRNA Poly(I:C) using a comercial microarray platform from Agilent. Chicken erythrocytes were isolated from blood by twice Ficoll 1.007 density gradient centrifugations. For primary cell culture, erythrocytes were resuspended in DMEM (PAA Laboratories) supplemented with 10% heat-inactivated fetal bovine serum (FBS, PAA Laboratories) and the antibiotic Primocin (100 μg/ml, Invivogen) at a density of 7.5x106 cells/ml in six well cell culture plates (NUNC) and cultured at 37ºC and 5% CO2. Erythrocytes were stimulated with LPS from E. coli (serotype 0111:B4, Sigma) and Poly(I:C) (Invivogen) at 50 μg/ml, and with peptidoglycan from E.coli (0111:B4, Invivogen) at 5 μg/ml. All culture plates were incubated for 12h. Total RNA was extracted from the cultures using 1 ml of Tri Reagent (Sigma) following the manufacturer’s instructions with minor modifications. Quantity and integrity was analyzed by Nanodrop1000 (ThermoScientific) and Bioanalyzer 2100 (Agilent Technologies) respectively. Three biological replicates were used.
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