Open Access Highly Accessed Methodology article

TE-array—a high throughput tool to study transposon transcription

Veena P Gnanakkan1, Andrew E Jaffe2, Lixin Dai3, Jie Fu4, Sarah J Wheelan45, Hyam I Levitsky467, Jef D Boeke1348* and Kathleen H Burns1489*

Author Affiliations

1 The Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building (MRB) Room 469, Baltimore, MD 21205, USA

2 The Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD, USA

3 Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Broadway Research Building, Room 339, Baltimore, MD 21205, USA

4 Department of Oncology, The Johns Hopkins University School of Medicine, Bunting Blaustein Cancer Research Building, Suite 4M51, 1650 Orleans St, Baltimore, MD 21287, USA

5 Department of Biostatistics, The Bloomberg School of Public Health, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

6 Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

7 Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

8 High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

9 Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

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BMC Genomics 2013, 14:869  doi:10.1186/1471-2164-14-869

Published: 10 December 2013

Additional files

Additional file 1: Figure S1:

(Left) Array design. Mouse or human specific TE consensus sequences were tiled with 60 bp probes. (1) TE families with consensus sequence less than 1 kb long were tiled every 14-15 bp with overlapping probes; (2) those greater than 1 kb long were tiled with probes sequentially offset in 30- 45 bp increments. (Right) Poly-A RNA (strand 1) was reverse transcribed to double stranded cDNA using MMLV RT (strands 2 and 3). T7 promoter was ligated to the 3′ end corresponding to poly-A, and T7 was used to generate single stranded, labeled cRNA. RNA was labeled using Cy-dye labeled Cytosine (strand 4).

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Additional file 2: Figure S2:

A) Technical replicates of the mouse N3D cell line. Four replicate TE-array hybridizations were performed with aliquots of RNA extracted from one cell culture. Plotted are pairwise correlations showing the behavior of all probes for each replicate type. B) Three technical replicates of RNA from the N1G cell line. C) Biological replicates. Four independent N3D cell cultures were expanded for RNA extraction and TE-array hybridization. D) Six biological replicates of N1G cells.

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Additional file 3: Table S1:

A: Replicates, B: Tissues.

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Additional file 4: Figure S3:

Tissue specific gene expression. As a control for reverse transcription and hybridization conditions, 100 genes were chosen and an array probe placed in each gene exon. Shown are M value (log2 ratio) plots for two testis specific genes, Brdt (bromodomain testis-specific protein) (A) and Theg (testicular haploid expressed gene) (B).

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Additional file 5: Figure S4:

Intra- and Inter-tissue clustering of TE-array and gene expression (GE) data. Multidimensional scaling applied to Euclidean distance was used to categorize tissues using A) TE-array and B) traditional gene expression microarray data.

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Additional file 6: Table S2:

The Excel worksheet has 4 tabs corresponding to different versions of TE-array. Abbreviations denote the species (hs, Homo sapiens; mm, Mus musculus) and strand (as, antisense strand; ss sense strand) of the version. Each list provides the probe ID and its genomic copy number. Corresponding sequences can be downloaded from the manufacturer’s site.

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