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Sample GSM289682 Query DataSets for GSM289682
Status Public on Aug 25, 2008
Title Hues13-1
Sample type RNA
 
Source name ES cells_ undifferentiated
Organism Homo sapiens
Characteristics at pluripotent stage: YES
Stem Cell Matrix: core dataset
SCM core sNMF cluster: 5
Growth protocol in vitro preparations were harvested, derived, differentiated and/or grown according to published protocols for the respective lines and samples. For further details and references please refer to Supplementary Tables 1 - 8 of the manuscript Regulatory networks define phenotypic classes of human stem cell lines
Extracted molecule total RNA
Extraction protocol Depending on the lab that suplied samples, different extraction methods were used according to standard/manufacturers protocols: TriZOL extraction, Quiagen Rneasy Mini Kit or Ambion Mirvana
Label biotin
Label protocol total RNA samples were quality assessed using Nanodrop Spectrophotometer, Invitrogen Qbit Spectrophotometer and the Agilent Bioanalyzer. Samples were then amplified one round, using an RNA Amplification Kit (Ambion) according to the manufacturer's instructions. The resulting purified cDNA product of was resuspended and dried down in a speedvac centifuge. cDNA was then converted to cRNA using an in vitro transcription kit according to the manufacturer's instructions (Roche),followed by another round of QC with Nanodrop/Bioanalyzer
 
Hybridization protocol Sucessfully labeled cRNA samples were then hybridized to Human Ref-8 BeadChips and Human WG6 BeadChips (Illumina) according to the manufacturer's instructions (approximately 23,000 identical gene probes are represented on both array designs), using equipment specified by the manufacturer (Illumina). Briefly, 850 ng biotin-labeled cRNA in 11.3 µl nuclease-free water was adjusted to 34 µl through the addition of 22.7 µl of 5:3 HybE1 buffer/formamide. The sample was heated at 65°C for 5 min, allowed to cool to room temperature, and then immediately added to a single array of an 8-array Human Ref-8 BeadChip. Once all 8 samples were added to each BeadChip, it was sealed in a Hyb Cartridge and incubated for 16 h at 55°C with rotation in an Illumina hybridization oven (rotation setting 5). Following overnight hybridization, BeadChips were moved to a slide rack and serially washed using gentle rotation in glass staining dishes filled with a) 250 ml Illumina Wash Buffer×5 min, b) 250 ml 100% ethanol×10 min, c) 250 ml Illumina Wash Buffer×2 min. BeadChips were then blocked for 10 min in 4 ml Block E1 buffer (Illumina), followed by staining for 10 min in 1 µg/ml Streptavidin-Cy3 conjugate (GE Healthcare) in Block E1 buffer. Stained BeadChips were finally washed using gentle rotation in a glass staining dish filled with 250 ml Illumina Wash Buffer×5 min. BeadChips were dried by centrifugation at 280×g for 4 min and stored in a light-tight box until reading.
Scan protocol Processed arrays were read using a BeadStation array reader (Illumina) according to the manufacturer's instructions. Scan settings were for single color (green) scanning.
Description 1401771144A
embryonic stem cell line
Data processing All arrays (Human Ref-8 BeadChips and Human WG6 BeadChips) were uploaded in BeadStudio version 1.5.1.3 and the intensity values for all 23,000 identical probes on both array designs were extracted; Normalization = none; Array Content = Human_RefSeq-8.xml; Error Model = none; uploaded into R/Bioconductor; Quantile normalized with R/package Affy
 
Submission date May 20, 2008
Last update date Aug 25, 2008
Contact name Franz-Josef Mueller
E-mail(s) fj.mueller@zip-kiel.de
Phone 0431-8006272
Fax 0431-8006272
Organization name Zentrum für Integrative Psychiatrie
Lab Loring Lab Germany
Street address Niemannsweg 147
City Kiel
State/province Schleswig-Holstein
ZIP/Postal code 24105
Country Germany
 
Platform ID GPL2700
Series (1)
GSE11508 Regulatory networks define phenotypic classes of human stem cell lines

Data table header descriptions
ID_REF
VALUE raw data was filtered for probes with >= 0.99 detection level as computed by BeadStudio version 1.5.1.3, then quantile normalized, then values <= 100 were set to 100, then the data was filtered for probes with more than 3 fold change over the entire dataset resulting in 15 205 probes.

Data table
ID_REF VALUE
GI_14141192-S 10305.5347
GI_4507728-S 10523.14064
GI_4507744-S 13000.96027
GI_10047089-S 100
GI_10047091-S 213.493379
GI_10047093-S 699.860274
GI_10047099-S 352.2383562
GI_10047103-S 4919.393607
GI_10047105-S 109.1358447
GI_10047123-S 544.9401826
GI_10047133-A 102.2819635
GI_10092578-S 100
GI_10092585-S 160.9369863
GI_10092596-S 370.6990868
GI_10092600-S 708.3347032
GI_10092611-A 229.2141553
GI_10092616-S 151.8022831
GI_10092618-S 1225.785845
GI_10092638-S 202.6634703
GI_10092658-S 121.6054795

Total number of rows: 15205

Table truncated, full table size 375 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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