cell type: cultured lymphoblastoid cells disease state: global developmental delay and autistic features
Growth protocol
EBV-transformed lymphoblast cell lines from patients, carriers, and unrelated normal controls, according to protocols approved by the institutional review board.
Extracted molecule
total RNA
Extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label
biotin
Label protocol
1 ug total RNA was used as starting material. rRNA reduction, 1st cycle dscDNA, cRNA (by IVT), and 2nd cycle 1st strand cDNA synthesis, cRNA hydrolysis, fragmentation (5.5ug single strand DNA) and terminal labeling were all done according to the standard Affymetrix whole transcript sense target labeling protocols.
Hybridization protocol
A hybridization cocktail was prepared according to Affymetrix's whole transcript sense target labeling protocols. The whole cocktail, including around 5.5 ug fragmented and labelled DNA, was hybridized on Human Exon 1.0 ST arrays. GeneChips were washed in the Affymetrix automated fluidic station.
Scan protocol
GeneChips were scanned using the Affymetrix G7 3000 scanner.
Description
Gene expression data from index patient.
Data processing
The open source R/Bioconductor packages (Fred Hutchinson Cancer Research Center, Seattle, WA, USA) were employed to normalize the data by GC Robust Multi-array Average (GC-RMA) algorithm. Further analyses were performed using PARTEK Genomics Suite (Partek® software, Partek Inc., St. Louis, MO, USA.). We used MATLAB (The Math Works, Inc., Natic, MA) and PARTEK Genomics Suite for the statistical analysis.
Exons included in the analysis: core Genome build: hg18
Whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) and whole blood from patients with global developmental delay and autistic features and unrelated normal controls
