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Gene expression analysis upon lncRNA DDSR1 knockdown in human fibroblasts.

Jia L, Sun Z, Wu X, Misteli T, Sharma V - Genom Data (2015)

Bottom Line: Since lncRNAs also modulate gene expression, we identified gene expression changes upon DDSR1 knockdown in human fibroblast cells.Gene expression analysis after RNAi treatment targeted against DDSR1 revealed 119 genes that show differential expression.Here we provide a detailed description of the microarray data (NCBI GEO accession number GSE67048) and the data analysis procedure associated with the publication by Sharma et al., 2015 in EMBO Reports [1].

View Article: PubMed Central - PubMed

Affiliation: CCR Collaborative Bioinformatics Resource (CCBR), National Cancer Institute, NIH, Bethesda, MD 20892, USA.

ABSTRACT
Long non-coding RNAs (lncRNAs) play important roles in regulating diverse biological processes including DNA damage and repair. We have recently reported that the DNA damage inducible lncRNA DNA damage-sensitive RNA1 (DDSR1) regulates DNA repair by homologous recombination (HR). Since lncRNAs also modulate gene expression, we identified gene expression changes upon DDSR1 knockdown in human fibroblast cells. Gene expression analysis after RNAi treatment targeted against DDSR1 revealed 119 genes that show differential expression. Here we provide a detailed description of the microarray data (NCBI GEO accession number GSE67048) and the data analysis procedure associated with the publication by Sharma et al., 2015 in EMBO Reports [1].

No MeSH data available.


Related in: MedlinePlus

Comparison between raw vs. normalized probe intensity. A) Boxplot of raw data. B) Boxplot of log2 RMA normalized intensity data. Each box corresponds to one array. Samples are in the following order: siNS (3 replicates) and siDDSR1 (3 replicates). (C) Histogram for probe intensity distribution after log2 RMA normalization. Each line represents one sample 3 replicates each of siNS and siDDSR1.
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f0005: Comparison between raw vs. normalized probe intensity. A) Boxplot of raw data. B) Boxplot of log2 RMA normalized intensity data. Each box corresponds to one array. Samples are in the following order: siNS (3 replicates) and siDDSR1 (3 replicates). (C) Histogram for probe intensity distribution after log2 RMA normalization. Each line represents one sample 3 replicates each of siNS and siDDSR1.

Mentions: Probe cell intensity (.CEL) files were imported into the R package and normalized using the Robust Multiarray Averaging (RMA) normalization method [2]. Microarray quality control was performed on the raw and normalized data. Signal Intensity before and after log2 RNA signal transformation is shown in (Fig. 1). Distribution of probe intensity values assessed with normalized data did not show any significant outliers (Fig. 1C). To investigate the intensity bias and to reduce the signal-to-noise ratio MA plot was applied to raw and normalized data as shown in (Fig. 2). The relation between the 2 groups (siNS and siDDSR1) after RMA normalization is presented in (Fig. 2C).


Gene expression analysis upon lncRNA DDSR1 knockdown in human fibroblasts.

Jia L, Sun Z, Wu X, Misteli T, Sharma V - Genom Data (2015)

Comparison between raw vs. normalized probe intensity. A) Boxplot of raw data. B) Boxplot of log2 RMA normalized intensity data. Each box corresponds to one array. Samples are in the following order: siNS (3 replicates) and siDDSR1 (3 replicates). (C) Histogram for probe intensity distribution after log2 RMA normalization. Each line represents one sample 3 replicates each of siNS and siDDSR1.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4664778&req=5

f0005: Comparison between raw vs. normalized probe intensity. A) Boxplot of raw data. B) Boxplot of log2 RMA normalized intensity data. Each box corresponds to one array. Samples are in the following order: siNS (3 replicates) and siDDSR1 (3 replicates). (C) Histogram for probe intensity distribution after log2 RMA normalization. Each line represents one sample 3 replicates each of siNS and siDDSR1.
Mentions: Probe cell intensity (.CEL) files were imported into the R package and normalized using the Robust Multiarray Averaging (RMA) normalization method [2]. Microarray quality control was performed on the raw and normalized data. Signal Intensity before and after log2 RNA signal transformation is shown in (Fig. 1). Distribution of probe intensity values assessed with normalized data did not show any significant outliers (Fig. 1C). To investigate the intensity bias and to reduce the signal-to-noise ratio MA plot was applied to raw and normalized data as shown in (Fig. 2). The relation between the 2 groups (siNS and siDDSR1) after RMA normalization is presented in (Fig. 2C).

Bottom Line: Since lncRNAs also modulate gene expression, we identified gene expression changes upon DDSR1 knockdown in human fibroblast cells.Gene expression analysis after RNAi treatment targeted against DDSR1 revealed 119 genes that show differential expression.Here we provide a detailed description of the microarray data (NCBI GEO accession number GSE67048) and the data analysis procedure associated with the publication by Sharma et al., 2015 in EMBO Reports [1].

View Article: PubMed Central - PubMed

Affiliation: CCR Collaborative Bioinformatics Resource (CCBR), National Cancer Institute, NIH, Bethesda, MD 20892, USA.

ABSTRACT
Long non-coding RNAs (lncRNAs) play important roles in regulating diverse biological processes including DNA damage and repair. We have recently reported that the DNA damage inducible lncRNA DNA damage-sensitive RNA1 (DDSR1) regulates DNA repair by homologous recombination (HR). Since lncRNAs also modulate gene expression, we identified gene expression changes upon DDSR1 knockdown in human fibroblast cells. Gene expression analysis after RNAi treatment targeted against DDSR1 revealed 119 genes that show differential expression. Here we provide a detailed description of the microarray data (NCBI GEO accession number GSE67048) and the data analysis procedure associated with the publication by Sharma et al., 2015 in EMBO Reports [1].

No MeSH data available.


Related in: MedlinePlus