All High Throughput Experiments > Large Scale Dataset Card

Large Scale dataset: Cultured Cell Collection

The cultured cell collection includes the top differentially expressed genes in 131 human primary and stem cells, purchased from different cell supplying companies, grown and analyzed by BioTime.

Total RNA was extracted from cells, using Qiagen RNeasy mini kits, according to the manufacturer’s instructions. RNA concentrations were determined using a Beckman DU530 or Nanodrop spectrophotometer and RNA quality was determined by denaturing agarose gel electrophoresis or using an Agilent 2100 bioanalyzer.

Whole-genome expression analysis was carried out using Illumina Human HT-12 v4 BeadArrays (GPL10558). Total RNA was linearly amplified and biotin-labeled, using Illumina TotalPrep kits (Life Technologies, Temecula, CA, USA). The amplified, labeled RNA was quality-controlled using an Agilent 2100 Bioanalyzer.  The RNA was then hybridized to Illumina BeadChips, processed, and read using a BeadStation array reader, according to the manufacturer’s instructions (Illumina, San Diego, CA, USA).

The microarray raw data was normalized using the  Robust Multi-array Average (RMA) normalization procedure. Low-intensity probes and probes with high variance among replicates were omitted. For each cell, differentially expressed genes were calculated against a weight average of all other cells in the collection.  The top-ranked log2 differentiated genes (fold change>=2) are listed for each sample.  The full list of all the genes with fold change >2 is available upon request.

Microarray Analysis
HT-12 V4.0 expression beadchip [Illumina - GPL10558]
In Vitro
Large Scale dataset: Cultured Cell Collection