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Sample GSM2091099 Query DataSets for GSM2091099
Status Public on Nov 04, 2016
Title SOX2_rep3
Sample type RNA
 
Source name GSC-11 cell line, siRNA against human Sox2
Organism Homo sapiens
Characteristics cell line: GSC-11
sirna: siRNA against human Sox2
Treatment protocol To inhibit Sox2 expression, transient transfection were performed using si-Sox2 or si-scramble (Ambion) according to the manufacturer's instructions using Lipofectamine 2000 (Invitrogen). The cells were then cultured for 72 h after transfections and subjected to RNA extraction
Growth protocol GSC11 cells were maintained in Dulbecco's modified Eagle's medium/nutrient mixture F12 supplemented with B27 (Invitrogen, Carlsbad, CA), epidermal growth factor, and basic fibroblast growth factor (20 ng/mL each; Sigma-Aldrich, St Louis, MO.
Extracted molecule total RNA
Extraction protocol Total cellular RNA was isolated from the cultured cells using Trizol reagent (Ambion) according to the manufacturers' protocols
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Agilent Technologies Scanner G2505C US82003505
Data processing Data were normalized with Bioconductor software using quantiles
 
Submission date Mar 16, 2016
Last update date Nov 04, 2016
Contact name Marta Maria Alonso Roldán
E-mail(s) mmalonso@unav.es
Organization name University Hospital of Navarra
Department Dpt of Pediatrics
Lab 2.03
Street address CIMA building , Pio XII 55
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL13607
Series (1)
GSE79302 Analysis of Sox2-regulated transcriptome in glioma stem cells

Data table header descriptions
ID_REF
VALUE Quantile-normalized log2 signal intensity

Data table
ID_REF VALUE
1 17.07014713
2 2.558292927
3 2.556587367
4 11.23330545
5 12.71518788
6 7.620269293
7 14.72042752
8 11.89572281
9 3.674567991
10 7.012359527
11 2.517878093
12 12.42967415
13 13.77556544
14 10.79772575
15 15.09348323
16 2.470495537
17 9.725491375
18 4.177949385
19 8.040134119
20 11.75864739

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.




Supplementary file Size Download File type/resource
GSM2091099_2_3_sox2_exp5.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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