Additional file 1:

Expression of mRNAs according to microarray analysis at different stages of oligodendrocyte and neuronal differentiation. Abbreviations are: bipotent progenitor cells, N/OP; GABAergic neurons, GABAN; oligodendrocyte progenitors, OLP; post-mitotic oligodendrocytes, PMO; myelinating oligodendrocytes: MYO). Probe IDs for targeted mRNA may be queried in the NRED database [102]. Information for targeted mRNAs shown includes Accession IDs, UniGene Common Name and Symbol and M-statistic, Fold Change, A- and B-statistic as calculated from microarray analysis.

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Additional file 2:

Expression of ncRNAs according to microarray analysis at different stages of oligodendrocyte and neuronal differentiation. Abbreviations are: bipotent progenitor cells, N/OP; GABAergic neurons, GABAN; oligodendrocyte progenitors, OLP; post-mitotic oligodendrocytes, PMO; myelinating oligodendrocytes: MYO). Probe IDs for targeted mRNA may be queried in the NRED database [102]. Information for targeted ncRNAs shown includes Accession IDs, M-statistic, Fold Change, A- and B-statistic as calculated from microarray analysis.

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Additional file 3:

QRT-PCR validation for microarray analysis of ncRNA expression in OL lineage elaboration. QRT-PCR analysis was performed to evaluate expression of 11 ncRNA across five cell types and corroborated microarray data in 48 (87%) of 55 instances.

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Additional file 4:

Noncoding RNAs associated with protein-coding genes. Noncoding transcript accession IDs are shown with associated protein-coding UniGene Common Name and Symbol and relationship of association (intronic, bidirectional, antisense). Evidence for positional conservation of ncRNA with homologous gene in the human genome (hg18) indicated.

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Additional file 5:

Noncoding RNA transcripts sequences predicted to fold into high confidence (P > 0.9) secondary structures according to RNAz. Chromosome coordinates and sequences are provided for region of expressed ncRNAs that are predicted to fold into conserved secondary structures. Predicted secondary structures according are provided in dot-bracket annotation (analysis conducted with Vienna RNA Package [101]). Selected high confidence structures are illustrated in Additional file 6.

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Additional file 6:

Rendered illustrations of the top five most stable secondary predicted structures in expressed ncRNAs. The five most predicted stable structures were rendered using CONTRAfold [99].

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Additional file 7:

Gomafu expression during GABAergic neuronal and progressive stages of OL lineage elaboration. (A) Relative expression of Gomafu during GABAN and OL differentiation (expression is relative to NSCs and error bars show standard deviation). Gomafu is exclusively downregulated in N/OPs, but upregulated in all other sampled cell stages. (B) In situ hybridization of sagittal adult mouse brain sections for Gomafu expression. Whole brain is shown in top left panel, hippocampus top right panel, coronal section of olfactory bulb in bottom left panel, and sagittal section of olfactory bulb and cortex in bottom right panel. Gomafu is expressed in the cortex (green arrow), hippocampus and mitral layer of the olfactory bulb (red arrow). Gomafu does not exhibit expression in the cerebellum (blue arrow). Images courtesy of the Allen Brain Atlas http://www.brain-map.org webcite.

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Additional file 8:

Snhg10 exhibits specific expression profiles in the adult mouse brain. Snhg10 exhibits a strong and broad expression throughout the whole mouse brain (A), with specific expression in Purkinje cells in the cerebellum (B) and hippocampus (C). Images courtesy of the Allen Brain Atlas http://www.brain-map.org webcite.

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Additional file 9:

mRNAs and ncRNAs that exhibit discordant expression trends during neuronal-glia fate switching. Table shows probe IDs that may be queried in the NRED database (Dinger et al., 2008), UniGene Common Name and Accession IDs and the discordant M-statistic and fold change associated with neural stem cell to GABAergic neuron (GABAN vs NSC) or oligodendrocyte progenitor (OLP vs NSC) transition as determined by microarray analysis.

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Additional file 10:

Expression of ncRNAs associated with ultraconserved elements. (A) Genomic context of the Dlx1 and Dlx2 gene (dark blue), the ncRNA Dlx1AS (AK132348; red) showing the position of ultraconserved element with previously described enhancer function (VISTA 422; green) and histogram of vertebrate conservation (dark blue). (B) Enhancer (VISTA 422) function driving reporter gene expression in the developing forebrain (red arrow) of 11.5 day mouse embryo [55]. Images courtesy of VISTA Enhancer Browser http://enhancer.lbl.gov/frnt_page.shtml webcite. (C) Expression of Dlx1AS (red) and Dlx1 gene (blue) during OL differentiation (expression is relative to NSCs and error bars show standard deviation). Dlx1AS ncRNA is upregulated in GABAN, similar to Dlx1, but downregulated in N/OPs and in different stages of OL differentiation (OLPs, PMOs, MYOs). (D) Genomic context of the Dlx5 and Dlx6 genes (blue) and the ncRNA Evf transcripts (1 and 2; red) showing the position of two ultraconserved elements with previously described enhancer function (VISTA 298) [55] and the enhancer described by Feng et al. [31]; green) and histogram of vertebrate conservation (dark blue). (E) Enhancer (VISTA 298) function driving reporter gene expression in the developing forebrain (red arrow) of 11.5 day mouse embryo [55]. Images courtesy of VISTA Enhancer Browser http://enhancer.lbl.gov/frnt_page.shtml webcite. (F) Expression of Evf (red) and Dlx5 gene (blue) during oligodendrogliogenesis (expression is relative to NSCs and error bars show standard deviation). The Evf ncRNA (red) is upregulated during GABAN, similar to Dlx5 (blue), but downregulated in N/OPs and later stages of oligodendrogliogenesis (OLPs, PMOs, MYOs). (G) Genomic context of the novel AK005755 ncRNA (red) showing the position of; ultraconserved element with previously described enhancer function (VISTA 433; green) and histogram of vertebrate conservation (dark blue). (H) Enhancer (VISTA 433) function driving reporter gene expression in the developing forebrain (red arrow) of 11.5 day mouse embryo [55]. Images courtesy of VISTA Enhancer Browser http://enhancer.lbl.gov/frnt_page.shtml webcite.

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Additional file 11:

Elaboration of PDGFRα on bipotent neuronal/oligodendrocyte precursors (N/OPs) independent of PDGF-AA application following propagation in vitro. N/OPs at 2 h (A-B) in vitro express the bHLH transcription factors, Olig2 and Mash1 (A), in addition to nestin (B). Immunofluorescence microscopic analysis reveals that PDGFRα is not initially expressed by this cellular species in our clonal culture paradigm. However, PDGFRα expression is unequivocally present at 24 h (C-D, arrowheads), demonstrating that N/OPs begin to acquire PDGFRα expression and responsiveness to PDGF-AA, which is required for proliferation and migration of OL progenitors following specification.

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Additional file 12:

Gene expression profiles of ncRNAs during oligodendrocyte differentiation. Correlation of expression profiles of ncRNAs with protein-coding gene markers during oligodendrogliogenesis. Genes with well-characterized roles in oligodendrogenesis were used to identify ncRNAs with correlated expression profiles (Pearson's coefficient > 0.9). This included Olig1 (A; purple) and Stm2 (B; red) that are differentially expressed in OLPs or Mobp (C; blue) or Melk (D; pink) that are differentially expressed during terminal differentiation to MYOs. NcRNA accession IDs are available in Additional file 13.

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Additional file 13:

Noncoding RNAs that exhibit concordant expression profiles with marker genes with well-characterized roles in neuronal and oligodendrocyte differentiation. Genes with well-characterized roles in oligodendrogliogenesis were used to identify ncRNAs with correlated expression profiles (Pearson's coefficient > 0.9). These genes include Olig1, Stmn2, Mobp, Melk, MOG, Mash1 and Nkx2-2. Illustration of selected expression profiles is shown in Additional file 13.

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Additional file 14:

The Sox8 gene and associated Sox8OT ncRNA share a dynamically modified chromatin domain. The genome browser view shows the bidirectional organization of the Sox8 gene (blue) and the Sox8OT ncRNA (red). A shared promoter region (shaded box) exhibits dynamic chromatin remodeling in embryonic stem cells (A; ES), embryonic fibroblasts (B; MEF) and neural progenitors (C; NP) [61]. The combination of active H3K4me3 (green histogram) and repressive H3K27me3 (red histogram) modified chromatin, observed in ES and MEF cells, is termed a bivalent domain and is indicative of a gene in a 'poised' state for activation. This is reflected in the low prevalence of H3K36me3 modified chromatin (blue histogram) that is normally associated with RNA Polymerase elongation. In NPs the bivalent domain has been resolved to an active H3K4me3 domain and the presence of H3K36me3 modified domains implies that both the Sox8 and Sox8OT transcripts are concordantly upregulated. Tpm; tags per million.

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Additional file 15:

The HDAC inhibitor TSA prevents the acquisition of secondary morphological features of differentiating PMOs with concurrent alteration in the expression profiles of ncRNAs under instructive conditions (CNTF treatment) and stochastic (CNTF naïve) for OL lineage maturation. (A-D) Immunofluorescence micrographs demonstrating the profiles of OL lineage species in the absence (A, B) or presence (C, D) of TSA at T1 (24 h, A, C) and T2 (48 h, B, D) in the presence of CNTF with concurrent PDGF-AA factor withdrawal. (E, F) The effects of TSA application on comparative expression profiles of ncRNAs as assessed at T1 (E) and at T2 (F) in relation to the timing of TSA exposure in the experimental conditions. (G-K) Immunofluorescence micrographs demonstrating the profiles of OL lineage species in the absence (G, H) or presence (J, K) of TSA at T1 (24 h, G, J) and T2 (48 h, H, K) in the presence PDGF-AA factor withdrawal only. (L, M) The effects of TSA application on comparative expression profiles of ncRNAs assessed at T1 (L) and at T2 (M) in relation to the timing of TSA exposure in the experimental conditions.

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Additional file 16:

List of ncRNA primers used in the validation of microarray results by QRT-PCR.

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