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Sample GSM1269703 Query DataSets for GSM1269703
Status Public on Oct 22, 2014
Title F_Control_41_ethanol
Sample type RNA
 
Source name LCLs from non-alcoholic_ethanol treatment
Organism Homo sapiens
Characteristics source subject id: 41
subject status: non-alcoholic (control)
subject gender: female
cell line: lymphoblastoid cell line (LCL)
treated with: 75mM ethanol for 24h
labelling batch: 3
Treatment protocol Cells were cultured in the absence or presence of 75 mM ethanol for 24 h
Growth protocol 2 x 10^6 LCLs from each of 21 alcoholics and 21 non-alcoholics were seeded in 10 ml of RPMI1640 medium supplemented with 15% FBS, 2 mM glutamine, 50 U/ml penicillin, and 50 µg/ml streptomycin.
Extracted molecule total RNA
Extraction protocol cells were harvested and lysed with buffer RLT, supplied in the Qiagen RNeasy kit, and RNA extractions were conducted per the manufacturer’s protocol
Label biotin
Label protocol Reverse transcription and labeling used the Affymetrix 3’ IVT labeling kit and protocols (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara). Samples were labeled in groups balanced by sex and phenotype to the extent possible; pairs of treated and untreated samples from the same individual were labeled and hybridized at the same time.
 
Hybridization protocol Samples were hybridized to Affymetrix HG U133 Plus 2 GeneChips® for 17 h, then washed and stained using the standard Affymetrix protocols.
Scan protocol GeneChips® were scanned using an Affymetrix Model 3000 scanner controlled by GCOS software (Affymetrix, Santa Clara, CA).
Description HE17H062
Data processing MAS5 signals and detection calls were generated by GCOS and scaled to 1000.
 
Submission date Nov 20, 2013
Last update date Oct 24, 2014
Contact name Jeanette Nance McClintick
E-mail(s) jnmcclin@iu.edu
Organization name Indiana University School of Medicine
Department Biochemistry & Molecular Biology
Lab Center for Medical Genomics
Street address 635 Barnhill Dr.
City Indianapolis
State/province IN
ZIP/Postal code 46202
Country USA
 
Platform ID GPL570
Series (1)
GSE52553 Ethanol treatment of lymphoblastoid cell lines from alcoholics and non-alcoholics causes many subtle changes in gene expression

Data table header descriptions
ID_REF
VALUE MAS5
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 1418.79 P 0.000389797
AFFX-BioB-M_at 2025.82 P 4.42873e-05
AFFX-BioB-3_at 1250.29 P 7.00668e-05
AFFX-BioC-5_at 4610.45 P 5.16732e-05
AFFX-BioC-3_at 5879.6 P 7.00668e-05
AFFX-BioDn-5_at 10337.8 P 4.42873e-05
AFFX-BioDn-3_at 17606.3 P 7.00668e-05
AFFX-CreX-5_at 53589.8 P 5.16732e-05
AFFX-CreX-3_at 63570.5 P 4.42873e-05
AFFX-DapX-5_at 2153.76 P 4.42873e-05
AFFX-DapX-M_at 4761.27 P 0.000169227
AFFX-DapX-3_at 9704.83 P 5.16732e-05
AFFX-LysX-5_at 430.422 P 6.02111e-05
AFFX-LysX-M_at 615.998 P 0.000389797
AFFX-LysX-3_at 1502.34 P 4.42873e-05
AFFX-PheX-5_at 683.765 P 4.42873e-05
AFFX-PheX-M_at 1005.04 P 9.4506e-05
AFFX-PheX-3_at 1207.45 P 4.42873e-05
AFFX-ThrX-5_at 466.457 P 0.00010954
AFFX-ThrX-M_at 939.201 P 5.16732e-05

Total number of rows: 54675

Table truncated, full table size 1637 Kbytes.




Supplementary file Size Download File type/resource
GSM1269703_HE17H062.CEL.gz 4.8 Mb (ftp)(http) CEL
GSM1269703_HE17H062.CHP.gz 295.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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