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Sample GSM300493 Query DataSets for GSM300493
Status Public on Jul 03, 2008
Title Transcriptome of HEK293T cells
Sample type RNA
Source name HEK293T cells
Organism Homo sapiens
Characteristics Human embryonic kidney (HEK293T) cells
Growth protocol HEK 293T cells were cultured in parallel in 2*150 cm3 flasks with DMEM (penicillin-streptomycin) (Gibco) supplemented with 10% Fetal Calf Serum (FCS) (Biochrom) and Glutamax (1x) (Gibco). At passage 20 (confluent state), cells were trypsinized, washed off in PBS, pelleted and resuspended in 2 ml lysis solution RLT (Qiagen).
Extracted molecule total RNA
Extraction protocol Total RNA was then extracted from ~ 20 x 106 cells per sample (2*HEK and 2*B cells samples) using RNeasy Midi extraction kit (Qiagen) by following the manufacturer’s instructions. DNA was removed using the “on column digestion” protocol of the RNeasy Midi extraction kit (Qiagen). Total RNA quality was assessed by spectrophotometry (Nanodrop) and gel electrophoresis (1% agarose)
Label Biotin
Label protocol Biotin-labelled cRNA was generated using a linear amplification kit (Ambion #IL1791) starting with 500 ng of DNA-free, quality-checked total RNA of each sample as input (see RNA preparation)
Hybridization protocol Chip hybridisations, washing, and Cy3-streptavidin (Amersham Biosciences) staining were performed on the Illumina BeadStation 500 platform employing reagents and following protocols supplied by the manufacturer. cRNA samples were hybridized as biological and technical duplicates on Illumina HumanRef8 V2.0 BeadChips.
Scan protocol scanning was performed on the Illumina BeadStation 500 platform
Description cRNA samples were hybridized as biological and technical duplicates on Illumina HumanRef8 V2.0 BeadChips.

HEK2-1raw.txt: HEK biological replicate 1, technical replicate 1
HEK2-2raw.txt: HEK biological replicate 1, technical replicate 2
HEK4-1raw.txt: HEK biological replicate 2, technical replicate 1
HEK4-2raw.txt: HEK biological replicate 2, technical replicate 2
Data processing Raw expression data (BeadSummary gene profile files), without normalization, were extracted from the manufacturer’s Illumina BeadStudio application software 1.0. Further processing of the data was done within the R / Bioconductor statistical analysis software package. We calculated the Pearsons product moment correlation coefficient on the non-normalized data sets to remove outliers and to check for integrity of the experiments (r>=0.98), followed by the computation of intra-chip pair-wise scatter-plots for each probe. The raw data sets were then normalized using quantile normalization.
Submission date Jun 26, 2008
Last update date Aug 18, 2008
Contact name Marc Sultan
Organization name Max Planck Institute for molecular genetics
Street address Ihnestr. 73
City Berlin
ZIP/Postal code 14195
Country Germany
Platform ID GPL6104
Series (1)
GSE11892 A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

Data table header descriptions
ID_REF dots in sequences denote ambiguous base calls
VALUE Normalized mean intensity value

Data table
ILMN_1804663 225.375
ILMN_1651799 2900.55
ILMN_1782558 38.3
ILMN_1812262 108.425
ILMN_1712803 1175.325
ILMN_1774757 63.9
ILMN_1712730 59.125
ILMN_1813561 47.175
ILMN_1761511 43.9
ILMN_1815941 117.025
ILMN_1711451 45.525
ILMN_1728255 45.7
ILMN_1723582 53.175
ILMN_1796374 64.75
ILMN_1713272 43.525
ILMN_1674380 542.525
ILMN_1660582 439.775
ILMN_1717492 54.225
ILMN_1811370 40.25
ILMN_1652243 49.3

Total number of rows: 20569

Table truncated, full table size 397 Kbytes.

Supplementary file Size Download File type/resource
GSM300493_HEK2_1raw.txt.gz 149.3 Kb (ftp)(http) TXT
GSM300493_HEK2_2raw.txt.gz 149.0 Kb (ftp)(http) TXT
GSM300493_HEK4_1raw.txt.gz 149.0 Kb (ftp)(http) TXT
GSM300493_HEK4_2raw.txt.gz 148.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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