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Sample GSM1269657 Query DataSets for GSM1269657
Status Public on Oct 22, 2014
Title F_Control_19_ethanol
Sample type RNA
 
Source name LCLs from non-alcoholic_ethanol treatment
Organism Homo sapiens
Characteristics source subject id: 19
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 HE17H014
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 1131.32 P 0.000662269
AFFX-BioB-M_at 1507.15 P 4.42873e-05
AFFX-BioB-3_at 1005.82 P 7.00668e-05
AFFX-BioC-5_at 3387.82 P 5.16732e-05
AFFX-BioC-3_at 4089.65 P 4.42873e-05
AFFX-BioDn-5_at 8045.1 P 4.42873e-05
AFFX-BioDn-3_at 16087.9 P 8.14279e-05
AFFX-CreX-5_at 42744.2 P 5.16732e-05
AFFX-CreX-3_at 52584.7 P 4.42873e-05
AFFX-DapX-5_at 2374.01 P 4.42873e-05
AFFX-DapX-M_at 5050.05 P 0.000258358
AFFX-DapX-3_at 8702.84 P 5.16732e-05
AFFX-LysX-5_at 441.587 P 4.42873e-05
AFFX-LysX-M_at 635.748 P 0.000169227
AFFX-LysX-3_at 1310.45 P 4.42873e-05
AFFX-PheX-5_at 563.312 P 4.42873e-05
AFFX-PheX-M_at 885.566 P 7.00668e-05
AFFX-PheX-3_at 1004.92 P 4.42873e-05
AFFX-ThrX-5_at 409.544 P 0.000195116
AFFX-ThrX-M_at 903.304 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1639 Kbytes.




Supplementary file Size Download File type/resource
GSM1269657_HE17H014.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM1269657_HE17H014.CHP.gz 295.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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