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Sample GSM623461 Query DataSets for GSM623461
Status Public on Jan 12, 2011
Title Endoderm_passage6_mes1_rep2
Sample type RNA
Source name mouse embryonic stem cell-derived endoderm, P6
Organism Mus musculus
Characteristics strain: R1
cell type: embryonic stem cell
Treatment protocol The sorted Sox17-GFP(+) cells were split into 3 destinations: 1. RNA was collected (for an unpassaged, freshly-differentiated sample of endoderm) OR 2. Sox17-GFP(+) cells were serially passaged six times (P6) on mouse mesenchyme 1 OR 2. Sox17-GFP(+) cells were serially passaged six times (P6) on mouse mesenchyme 2
Growth protocol Mouse embryonic stem cells containing a Sox17-GFP construct were differentiated using growth factors (Activin A and Wnt3A) for six days to definitive endoderm. Sox17-GFP(+) cells were sorted using fluorescence-activated cell sorting (FACS).
Extracted molecule total RNA
Extraction protocol Sox17-GFP(+) cells were isolated by FACS in buffer containing PBS/5% FBS. Cells were spun for 5 minutes, 1000 rpm, and the supernatant was removed. RNA was then harvested using the Rneasy kit (Qiagen) according to the manufacturer's instructions.
Label biotin
Label protocol Total RNA was amplified and labeled using the Illumina TotalPrep RNA amplification kit (Ambion).
Hybridization protocol Samples were hybridized onto Illumina Mouse Ref8 version 2 BeadChips as per the manufacturer's instructions.
Scan protocol Arrays were scanned on an Illumina machine according to the manufacturer's instructions.
Description culture condition: co-culture with mesenchyme 1
Data processing Data were analyzed with BeadStudio analysis software (Illumina). Samples were normalized using Illumina's average normalization, with no background subtraction. The data were filtered for only genes for which the p value of detection was < 0.01.
Submission date Nov 15, 2010
Last update date Jan 12, 2011
Contact name Julie Beth Sneddon
Organization name Harvard University
Department Department of Stem Cells and Regenerative Biology
Lab Douglas Melton Lab
Street address 7 Divinity Avenue
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
Platform ID GPL6885
Series (1)
GSE25337 Gene expression data of Sox17-GFP(+) mouse definitive endoderm before and after expansion on mesenchyme.

Data table header descriptions
VALUE Average normalization, no background subtraction
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 643.009 0
ILMN_2721178 143.1606 0
ILMN_1227723 48.31425 0
ILMN_3033922 132.6335 0
ILMN_3092673 506.9152 0
ILMN_2730714 576.6829 0
ILMN_3162224 968.3412 0
ILMN_2808939 348.2148 0
ILMN_2634564 167.1212 0
ILMN_1216623 244.4442 0
ILMN_1215157 312.5978 0
ILMN_2734484 364.5218 0
ILMN_2952292 18.68231 0
ILMN_2660815 567.0926 0
ILMN_1243593 401.765 0
ILMN_1219797 80.05308 0
ILMN_1231132 112.4104 0
ILMN_2718462 43.61182 0
ILMN_2653881 168.9488 0
ILMN_2638061 25.83987 0

Total number of rows: 11097

Table truncated, full table size 259 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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