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Sample GSM2091097 Query DataSets for GSM2091097
Status Public on Nov 04, 2016
Title SOX2_rep1
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
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
VALUE Quantile-normalized log2 signal intensity

Data table
1 16.92045744
2 2.385326208
3 2.384311825
4 10.7097229
5 12.5319297
6 8.246014583
7 14.79310513
8 11.66944964
9 2.849958022
10 7.578395621
11 2.375044884
12 12.34945268
13 13.65425736
14 10.73832333
15 14.84303794
16 2.366652912
17 10.13690774
18 3.394958169
19 8.46988654
20 11.8443022

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.

Supplementary file Size Download File type/resource
GSM2091097_1_2_sox2_exp1.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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