Supplementary information

From the following article:

Mapping and sequencing of structural variation from eight human genomes

Jeffrey M. Kidd, Gregory M. Cooper, William F. Donahue, Hillary S. Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci, Eric Haugen, Troy Zerr, N. Alice Yamada, Peter Tsang, Tera L. Newman, Eray Tüzün, Ze Cheng, Heather M. Ebling, Nadeem Tusneem, Robert David, Will Gillett, Karen A. Phelps, Molly Weaver, David Saranga, Adrianne Brand, Wei Tao, Erik Gustafson, Kevin McKernan, Lin Chen, Maika Malig, Joshua D. Smith, Joshua M. Korn, Steven A. McCarroll, David A. Altshuler, Daniel A. Peiffer, Michael Dorschner, John Stamatoyannopoulos, David Schwartz, Deborah A. Nickerson, James C. Mullikin, Richard K. Wilson, Laurakay Bruhn, Maynard V. Olson, Rajinder Kaul, Douglas R. Smith & Evan E. Eichler

Nature 453, 56-64(1 May 2008)

doi:10.1038/nature06862

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Supplementary Information

The file contains extensive Supplementary Information with Supplementary Figures S1-S2, S4-S9. Supplementary Figures S3 and S10 are included in separate files.

Supplementary Figure S2

The file contains Supplementary Figure S2 with end-sequence mapping of fosmids against the human genome. All discordant fosmids mapping to the human genome are displayed individually for each library using the following color scheme: ABC7=green, ABC8=forestgreen, ABC10=blue, ABC13=cyan, G248=black, ABC9=purple, ABC11=red, ABC12=orange, and ABC14=hotpink. The end-sequence placements are mapped in the context of gaps within the assembly (purple) and segmental duplications (grey bars).

Supplementary Figure S3

The file contains Supplementary Figure S3 with end-sequence mapping of fosmids against the human genome. All discordant fosmids mapping to the human genome are displayed individually for each library using the following color scheme: ABC7=green, ABC8=forestgreen, ABC10=blue, ABC13=cyan, G248=black, ABC9=purple, ABC11=red, ABC12=orange, and ABC14=hotpink. The end-sequence placements are mapped in the context of gaps within the assembly (purple) and segmental duplications (grey bars).

Supplementary Figure S4

The file contains Supplementary Figure S4 with end-sequence mapping of fosmids against the human genome. All discordant fosmids mapping to the human genome are displayed individually for each library using the following color scheme: ABC7=green, ABC8=forestgreen, ABC10=blue, ABC13=cyan, G248=black, ABC9=purple, ABC11=red, ABC12=orange, and ABC14=hotpink. The end-sequence placements are mapped in the context of gaps within the assembly (purple) and segmental duplications (grey bars).

Supplementary Figure S10

The file contains Supplementary Figure S10 with sequenced Structural Variation and Gene Structure. A graphical representation for sequenced sites (n=266) of structural variation (miropeats view) is provided. Each alignment compares the human reference genome (top) with the sequenced structure of the fosmid clone.

Supplementary Table S1

The file contains Supplementary Table S1 showing concordant vs. discordant clone placement summary statistics.

Supplementary Table S2

The file contains Supplementary Table S2 showing one-end anchored (OEA) clone statistics.

Supplementary Table S3

The file contains Supplementary Table S3 with All ESP predicted sites of insertions and deletions with associated experimental validation (See Supplementary Material Section 12 for description of column headers)

Supplementary Table S4

The file contains Supplementary Table S4 with ESP predicted sites of insertion and deletion loci (non-redundant) across the fosmid libraries (See Supplementary Material Section 12 for description of column headers)

Supplementary Table S5

The file contains Supplementary Table S5 with genotyping results for a subset of ESP deletion variants based on analysis of genotypes from the llumina Human1M BeadChip

Supplementary Table S6

The file contains Supplementary Table S6 with ESP predicted inversion breakpoints

Supplementary Table S7

The file contains Supplementary Table S7 with merged inversion loci (non-redundant).

Supplementary Table S8

The file contains Supplementary Table S8 with large insertions of novel sequence confirmed by optical mapping.

Supplementary Table S9

The file contains Supplementary Table S9 with genbank accession IDs of sequenced clones.

Supplementary Table S10

The file contains Supplementary Table S10 with sequenced structural variants that affect exons of genes.

Supplementary Table S11

The file contains Supplementary Table S11 with summary statistics of fosmid end sequences.

Supplementary Table S12

The file contains Supplementary Table S12 with genotypes based on custom GoldenGate Assay and qPCR.

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