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Identification of PRDM2 regulated genes in quiescent C2C12 myoblasts.

Cheedipudi S, Gala HP, Puri D, Dhawan J - Genom Data (2015)

Bottom Line: Quiescent stem cells contribute to tissue homeostasis and repair in adult mammals.We identified a tumor suppressor PRDM2, as an epigenetic regulator induced in quiescent muscle stem cells as well as in cultured quiescent myoblasts.To delineate the functions of PRDM2 in muscle cells, we compared the gene expression profiles of control and PRDM2 knockdown myoblasts in growing, differentiating and quiescent conditions (GEO accession number: GSE 58676).

View Article: PubMed Central - PubMed

Affiliation: Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India ; Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.

ABSTRACT
Quiescent stem cells contribute to tissue homeostasis and repair in adult mammals. We identified a tumor suppressor PRDM2, as an epigenetic regulator induced in quiescent muscle stem cells as well as in cultured quiescent myoblasts. To delineate the functions of PRDM2 in muscle cells, we compared the gene expression profiles of control and PRDM2 knockdown myoblasts in growing, differentiating and quiescent conditions (GEO accession number: GSE 58676). To identify the direct targets of PRDM2 and the promoters co-associated with H3K9me2 (mark catalyzed by PRDM2), ChIP-Chip analysis was performed (GSE58748). In this report we discuss in detail the methodology used to identify PRDM2 regulated genes and classify them into potential direct and indirect targets.

No MeSH data available.


Related in: MedlinePlus

Example of probe intensity and distribution of signal (A) Histogram showing distribution of normalized Log2 ratios for all probes in PRDM2 ChIP-Chip data set.B. Scatter plot of normalized intensities of IP vs Input showing probe enrichment.
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f0010: Example of probe intensity and distribution of signal (A) Histogram showing distribution of normalized Log2 ratios for all probes in PRDM2 ChIP-Chip data set.B. Scatter plot of normalized intensities of IP vs Input showing probe enrichment.

Mentions: Slides were scanned on an Agilent scanner and images were analyzed using Agilent feature extraction software. Text files generated by Agilent feature extraction software were normalized by median blank subtraction, inter-array median normalization and dye bias normalization by DNA Analytics software. Whitehead per-array neighborhood algorithm was used to detect robust peaks corresponding to the DNA binding. Enrichment values for all probes were obtained by normalized log IP/Input and probes with p value ≤ 0.05 were considered for further analysis (Fig. 2). ChIP-Chip with PRDM2 antibody was performed with two biological replicates and one array was used for H3K9me2. The data were deposited in GEO with the accession number GSE58748.


Identification of PRDM2 regulated genes in quiescent C2C12 myoblasts.

Cheedipudi S, Gala HP, Puri D, Dhawan J - Genom Data (2015)

Example of probe intensity and distribution of signal (A) Histogram showing distribution of normalized Log2 ratios for all probes in PRDM2 ChIP-Chip data set.B. Scatter plot of normalized intensities of IP vs Input showing probe enrichment.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664777&req=5

f0010: Example of probe intensity and distribution of signal (A) Histogram showing distribution of normalized Log2 ratios for all probes in PRDM2 ChIP-Chip data set.B. Scatter plot of normalized intensities of IP vs Input showing probe enrichment.
Mentions: Slides were scanned on an Agilent scanner and images were analyzed using Agilent feature extraction software. Text files generated by Agilent feature extraction software were normalized by median blank subtraction, inter-array median normalization and dye bias normalization by DNA Analytics software. Whitehead per-array neighborhood algorithm was used to detect robust peaks corresponding to the DNA binding. Enrichment values for all probes were obtained by normalized log IP/Input and probes with p value ≤ 0.05 were considered for further analysis (Fig. 2). ChIP-Chip with PRDM2 antibody was performed with two biological replicates and one array was used for H3K9me2. The data were deposited in GEO with the accession number GSE58748.

Bottom Line: Quiescent stem cells contribute to tissue homeostasis and repair in adult mammals.We identified a tumor suppressor PRDM2, as an epigenetic regulator induced in quiescent muscle stem cells as well as in cultured quiescent myoblasts.To delineate the functions of PRDM2 in muscle cells, we compared the gene expression profiles of control and PRDM2 knockdown myoblasts in growing, differentiating and quiescent conditions (GEO accession number: GSE 58676).

View Article: PubMed Central - PubMed

Affiliation: Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India ; Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.

ABSTRACT
Quiescent stem cells contribute to tissue homeostasis and repair in adult mammals. We identified a tumor suppressor PRDM2, as an epigenetic regulator induced in quiescent muscle stem cells as well as in cultured quiescent myoblasts. To delineate the functions of PRDM2 in muscle cells, we compared the gene expression profiles of control and PRDM2 knockdown myoblasts in growing, differentiating and quiescent conditions (GEO accession number: GSE 58676). To identify the direct targets of PRDM2 and the promoters co-associated with H3K9me2 (mark catalyzed by PRDM2), ChIP-Chip analysis was performed (GSE58748). In this report we discuss in detail the methodology used to identify PRDM2 regulated genes and classify them into potential direct and indirect targets.

No MeSH data available.


Related in: MedlinePlus