NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2250270 Query DataSets for GSM2250270
Status Public on Jun 09, 2017
Title 667N_(HTA-2_0)
Sample type RNA
 
Source name adjacent-SCC
Organism Homo sapiens
Characteristics tissue type: Adjacent normal lung tissue
Stage: I
technology: Microarray
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from biological samples using miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA quantity was determined using the NanoDrop Spectrophotometer. RNA quality was checked using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Diegem, Belgium) and only RNAs with a RIN number >7 were taken forward for microarray experiments.
Label biotin
Label protocol Labeling has been made using standard Affymetrix protocols.
 
Hybridization protocol Hybridation has been made using standard Affymetrix protocols.
Scan protocol Scanning has been made using standard Affymetrix protocols.
Data processing Pre-processing of Affymetrix CEL-files was performed with Partek® Genomics Suite version 6.6 (Partek® GS) using the robust multi-chip analysis (RMA) algorithm, which performs background adjustment, quantile normalisation and probe summarisation {Irizarry, 2003 #2}. GC-content correction was used, as suggested by the default pipeline of Partek® GS. Gene level expression was estimated using mean of probe set log expression. Further analysis was performed in R/Bioconductor {Team, 2005 #3}.
probe group file: HTA-2_0.r1.pgf
meta-probeset file: HTA-2_0.na33.hg19.probeset.csv
 
Submission date Jul 25, 2016
Last update date Jun 09, 2017
Contact name Arnaud Muller
E-mail(s) arnaud.muller@lih.lu, arnaud.muller@lns.etat.lu
Organization name LIH
Department DONC
Lab GENPRO
Street address 84 Val Fleuri
City Luxembourg
ZIP/Postal code 1526
Country Luxembourg
 
Platform ID GPL17585
Series (2)
GSE84784 Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours [Affymetrix]
GSE84788 Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours

Data table header descriptions
ID_REF
VALUE RMA signal from Partek GS v.6.6

Data table
ID_REF VALUE
2824546_st 12.1962
2824549_st 11.7284
2824551_st 12.3834
2824554_st 12.1587
2827992_st 10.9878
2827995_st 11.1366
2827996_st 11.1432
2828010_st 8.61749
2828012_st 10.3294
2835442_st 9.67077
2835447_st 9.1409
2835453_st 10.239
2835456_st 12.2644
2835459_st 9.98596
2835461_st 7.76343
2839509_st 10.5441
2839511_st 9.71871
2839513_st 10.7087
2839515_st 8.52532
2839517_st 10.7311

Total number of rows: 914585

Table truncated, full table size 22489 Kbytes.




Supplementary file Size Download File type/resource
GSM2250270_667N_HTA-2_0_.CEL.gz 23.5 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap