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Sample GSM1269661 Query DataSets for GSM1269661
Status Public on Oct 22, 2014
Title F_Alcoholic_20_ethanol
Sample type RNA
 
Source name LCLs from alcoholic_ethanol treatment
Organism Homo sapiens
Characteristics source subject id: 20
subject status: Alcoholic
subject gender: female
cell line: lymphoblastoid cell line (LCL)
treated with: 75mM ethanol for 24h
labelling batch: 1
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 HE17H018
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 1310.56 P 0.000581214
AFFX-BioB-M_at 1795.95 P 4.42873e-05
AFFX-BioB-3_at 1191.22 P 6.02111e-05
AFFX-BioC-5_at 3675.36 P 5.16732e-05
AFFX-BioC-3_at 4590.86 P 4.42873e-05
AFFX-BioDn-5_at 9694.4 P 4.42873e-05
AFFX-BioDn-3_at 16732.7 P 6.02111e-05
AFFX-CreX-5_at 50904.2 P 5.16732e-05
AFFX-CreX-3_at 58092.1 P 4.42873e-05
AFFX-DapX-5_at 1662.88 P 5.16732e-05
AFFX-DapX-M_at 3965.49 P 0.000258358
AFFX-DapX-3_at 7056.62 P 5.16732e-05
AFFX-LysX-5_at 385.11 P 6.02111e-05
AFFX-LysX-M_at 488.777 P 0.000509415
AFFX-LysX-3_at 1136.48 P 4.42873e-05
AFFX-PheX-5_at 597.951 P 4.42873e-05
AFFX-PheX-M_at 860.493 P 8.14279e-05
AFFX-PheX-3_at 856.911 P 4.42873e-05
AFFX-ThrX-5_at 313.752 P 0.00010954
AFFX-ThrX-M_at 734.806 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1639 Kbytes.




Supplementary file Size Download File type/resource
GSM1269661_HE17H018.CEL.gz 4.8 Mb (ftp)(http) CEL
GSM1269661_HE17H018.CHP.gz 296.6 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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