GEO series

8-chip high-resolution aCGH experiment NA15510 vs. NA18505

GSE9002 Homo sapiens (human) Genome variation profiling by genome tiling array 8 samples Submitted 2007/09/28 Platform GPL5821Platform GPL5816Platform GPL5819Platform GPL5814Platform GPL5820Platform GPL5817Platform GPL5815Platform GPL5818

At a glance

human · 8 samples

Organism: Homo sapiens (human)
Samples: 8 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and putatively European individual and identified shared and divergent SVs relative to the reference genome.

Read the full summary ↓

Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were deduced with a novel pooling strategy and computational analysis. Array-CGH was used for validation. Keywords: array CGH

This dataset

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Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE9002_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA102481. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 17901297) ↗

Samples in this study

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+ 8 more — browse all 8 samples with per-sample file links →

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