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Open Access Highly Accessed Research article

Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation

Biaoru Li1, Lianghao Ding2, Wei Li3, Michael D Story2 and Betty S Pace1*

Author Affiliations

1 Department Pediatrics, Georgia Health Sciences University, 1120 15th St. CN-4112, Augusta, GA 30912, USA

2 Department of Radiation Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA

3 Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA

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BMC Genomics 2012, 13:153  doi:10.1186/1471-2164-13-153

Published: 26 April 2012

Additional files

Additional file 1:

Figure S1. RNA quality check. Figure S4A Multiple regression analysis. Figure S5C Mitotic Roles of Polo-Like Kinasae signaling pathway. Figure S5D ATM signaling pathway.

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Additional file 2:

Table S1. Day 7 Illumina HumanWG-6V2 Expression BeadChip raw data. This file contains a table listing microarray raw data including the mean (M) and standard error (SEM) for each gene calculated from triplicate RNA samples extracted on day 7 from cells grown in the one-phase liquid culture system. Briefly, total RNA with amplified and biotin-labeled and then used for hybridization to the Illumina HumanWG-6V2 Expression BeadChip. Microarray raw data were generated on the Illumina Beadstation scanner.

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Additional file 3:

Table S2. Day 14 Illumina HumanWG-6V2 Expression BeadChip raw data. This file contains a table listing microarray raw data including the mean (M) and standard error (SE) for each gene calculated from triplicate RNA samples extracted on day 14 from cells cultured in the one-phase liquid culture system. Briefly, total RNA with amplified and biotin-labeled and then used for hybridization to the Illumina HumanWG-6V2 Expression BeadChip. Microarray raw data were generated on the Illumina Beadstation scanner.

Format: XLS Size: 2.5MB Download file

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Additional file 4:

Table S3. Day 21 Illumina HumanWG-6V2 Expression BeadChip raw data. This file contains a table listing microarray raw data including the mean (M) and standard error (SE) for each gene calculated from triplicate RNA samples extracted on day 21 from cells cultured in the one-phase liquid culture system. Briefly, total RNA with amplified and biotin-labeled and then used for hybridization to the Illumina HumanWG-6V2 Expression BeadChip. Microarray raw data were generated on the Illumina Beadstation scanner.

Format: XLS Size: 2.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Table S4. Day 28 Illumina HumanWG-6V2 Expression BeadChip raw data. This file contains a table listing microarray raw data including the mean (M) and standard error (SE) for each gene calculated from triplicate RNA samples extracted on day 28 from cells cultured in the one-phase liquid culture system. Briefly, total RNA with amplified and biotin-labeled and then used for hybridization to the Illumina HumanWG-6V2 Expression BeadChip. Microarray raw data were generated on the Illumina Beadstation scanner.

Format: XLS Size: 2.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Table S5. Differential gene expression generated by PCA. This file contains three tables listing genes with > 1.5-fold change in expression during erythroid maturation in our one-phase liquid culture system. PCA data show the log change; a positive value indicates decreased gene expression from day 7 to day 28 in contrast to increased gene expression indicated by a negative log change. The correlation score indicates the level of agreement between the specific globin gene profile curve and PCA values.

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Additional file 7:

Table S6. Gene Ontology analysis from profile-1, -2 and -3 gene subsets. This file contains a complete list of the DAVID GO terms generated for the three gene groups tested; the count number indicates how many genes were identified in the specific pathway by microarray analysis. The p values indicate the significance level for the specific pathways identified. The Benjamin score represents the adjusted multiple p values to take into account all genes involved in the pathways identified.

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Additional file 8:

Table S7. TESS, TFSEARCH, Weeder H and Fire analysis for profile-1 genes.

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Additional file 9:

Table S8. TESS, TFSEARCH, Weeder H and Fire analysis for profile-2 genes.

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Additional file 10:

Table S9. TESS, TFSEARCH, Weeder H and Fire analysis for profile-3 genes.

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Additional file 11:

Supplemental Methods. Method for the one-phase tissue culture system.

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