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Sample GSM1860458 Query DataSets for GSM1860458
Status Public on Aug 25, 2015
Title High grade tumor sample [CVA_Ast_23072014_(HTA-2_0)] exon-level
Sample type RNA
Source name Tumor sample
Organism Homo sapiens
Characteristics tissue: glia tissue
tumor grade: GBM
Treatment protocol A total of eight astrocytic tumors and two control tissues were collected during the period of 2012–2014: four low-grade Ast (three pilocytic Ast (PAst) and one diffuse Ast (DAst)) and four high-grade Ast (four glioblastoma multiforme (GBM)). Brain tumor samples were collected at surgery, snap frozen in liquid nitrogen and stored at −80 °C until use. All tumors were collected from children – one through 15 years of age – refer from the Children´s hospital, National Medical Center Century XXI, Mexican Institute of Social Security. All patients were from families with no history of cancer (de novo tumors)Control samples were obtained from pediatric patients (one boy and one girl) who had submitted to temporal lobe resection for epilepsy. Tumors were histopathologically classified by two pathologists according to a criteria established by the WHO.
Extracted molecule total RNA
Extraction protocol RNA was extracted from tissue samples using TRIzol (Ambion life technologies, Thermo Scientific Inc.) following the methodology described by Hongbao et al. 2008 and with certain modifications described by Vujovic et al. 2013. Briefly, tumor samples were homogenized in 1 ml of TRIZOL® Reagent (1ml per 50 mg of tissue), and incubated at room temperature (25°C) for 5 min. After that, we added 200 µl of chloroform (per ml TRIzol) and shake vigorously the samples for 15 sec. Then, samples were incubating at 4°C for 15 min and they were centrifuged at 12,000xg for 15 min (4°C). The aqueous phase, which corresponds to RNA was transferred to a new 1.5 ml tube and RNA was precipitated adding 500 µl isopropanol (per ml TRIzol) and incubating for 30 min at room temperature. After that, samples were centrifuged at 12,000xg (10 min) at 4°C, the supernatant was removed and pellet was washed once with 75% ethanol (1 ml/ml TRIzol), vortexed and centrifuged at 7,500xg for 5 min at 4°C. The final pellet was dissolved in 300-600 µl of RNase-free water and it was stored at -80 °C until use.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HTA 2.0 Array. Chips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using GeneArray Scanner G2500A.
Description Gene expression data from pediatric brain tumor grade V
Data processing For data analysis two softwares were used: Expression Console and Transcript Analysis Console. The first software allows us to perform a gene and exon-level normalization, and signaling summarization by evaluating QC values for the array. The second software allows evaluating gene and exon expiration between samples. Parameters used for the analysis were: One-Way Between-Subject ANOVA (Unpaired); Fold Change (linear) < -2 or Fold Change (linear) > 2; and ANOVA p-value (Condition pair) < 0.05.
Fold Change (linear) < -2 or Fold Change (linear) > 2; and ANOVA p-value (Condition pair) < 0.05.
Submission date Aug 24, 2015
Last update date Aug 25, 2015
Contact name Ruth Ruiz-Esparza
Phone (55) 56590883
Organization name Instituto Mexicano del Seguro Social
Department Pediatría
Lab Genética Humana
Street address Centro Médico Nacional Siglo XXI, IMSS, México,
City México.
State/province D.F.
ZIP/Postal code 06720
Country Mexico
Platform ID GPL17585
Series (1)
GSE72269 Differentially Expressed LncRNAs Might be Controlling Signaling Pathways by Establishing Interactions with mRNAs and MicroRNAs in Pediatric Astrocytoma
Alternative to GSM1859150 (gene-level analysis)

Data table header descriptions
VALUE log2-rma-alt-splice-dabg

Data table
JUC01000001.hg.1 7.10407 0.210476
JUC01000002.hg.1 4.91137 0.822839
JUC01000003.hg.1 7.98271 0.00415719
JUC01000004.hg.1 6.88387 0.0700861
JUC01000005.hg.1 9.04661 0.00265166
JUC01000006.hg.1 7.47975 0.128811
JUC01000007.hg.1 6.41279 0.217276
JUC01000008.hg.1 7.366 0.00132478
JUC01000009.hg.1 4.9752 0.0848345
JUC01000010.hg.1 4.81661 0.0198595
JUC01000011.hg.1 10.5859 0.000791038
JUC01000012.hg.1 7.62635 0.479238
JUC01000013.hg.1 11.802 4.56966e-07
JUC01000014.hg.1 9.84313 6.44588e-08
JUC01000015.hg.1 5.82492 0.187932
JUC01000016.hg.1 9.58195 0.000161149
JUC01000017.hg.1 6.57757 0.000403731
JUC01000018.hg.1 8.58399 0.103251
JUC01000019.hg.1 9.60573 0.000396464
JUC01000020.hg.1 9.60573 0.000396464

Total number of rows: 914585

Table truncated, full table size 31689 Kbytes.

Supplementary file Size Download File type/resource
GSM1860458_CVA_Ast_23072014_HTA-2_0_.CEL.gz 23.9 Mb (ftp)(http) CEL
GSM1860458_CVA_Ast_23072014_HTA-2_0_.rma-alt-splice-dabg.chp.gz 9.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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