NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM937092 Query DataSets for GSM937092
Status Public on Aug 07, 2012
Title HMLER GFP Rep2
Sample type RNA
 
Source name HMLER cells
Organism Homo sapiens
Characteristics cell line: HMLER
treatment: transduced with a scramble control GFP shRNAi
Growth protocol In vitro cultured according to published conditions
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol As per Affymetrix standard instructions
 
Hybridization protocol Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
Scan protocol The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
Description Gene expression data from HMLER cells transduced with a scramble control GFP shRNAi
Data processing Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
 
Submission date May 24, 2012
Last update date Mar 18, 2013
Contact name Marc Mendillo
Organization name Whitehead Institute for Biomedical Research
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL3921
Series (2)
GSE38232 HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers [gene expression]
GSE38912 HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers

Data table header descriptions
ID_REF
VALUE Log2 expression value from GCRMA

Data table
ID_REF VALUE
1007_s_at 7.336708628
1053_at 7.729532127
117_at 2.985114612
121_at 5.212929539
1255_g_at 2.594045342
1294_at 4.436798379
1316_at 2.858537287
1320_at 2.979023949
1405_i_at 4.493159697
1431_at 2.789699954
1438_at 2.894158865
1487_at 5.697753838
1494_f_at 3.262393709
1598_g_at 6.980008895
160020_at 6.588992183
1729_at 5.827932743
177_at 3.716876384
1773_at 4.109098826
179_at 4.943748587
1861_at 6.590707324

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM937092_MUMPS_p_Multi_P1_HT_HG-U133A_96-HTA_E06_440126.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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