Sequencing flow-sorted X chromosomes from a human female sample (CEU:NA07340) using the Illumina Genome Analyzer. X chromosome sequencing project

Chromosomes were prepared from a lymphoblastoid cell line (GM07340, within the National Institute of General Medical Sciences Human Genetic Cell Repository). Approximately 1.3 million X chromosomes were flow-sorted to a purity of ~90%. We generated an Illumina sequencing library with a median insert size of ~160 bp following random fragmentation and gel fractionation of purified chromosomal DNA. Paired-end sequencing of this library was carried out using the Illumina Genome Analyzer. We carried out purity-filtering (PF) to remove mixed reads, where two or more different template molecules are close enough on the surface of the flow-cell to form a mixed or overlapping cluster. No other filtering of reads has been carried out prior to submission. The data set contains approximately 278 million PF reads of 30-35 bp.