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Status |
Public on Oct 22, 2014 |
Title |
M_Alcoholic_44_ethanol |
Sample type |
RNA |
|
|
Source name |
LCLs from alcoholic_ethanol treatment
|
Organism |
Homo sapiens |
Characteristics |
source subject id: 44 subject status: Alcoholic subject gender: male cell line: lymphoblastoid cell line (LCL) treated with: 75mM ethanol for 24h labelling batch: 2
|
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.
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|
|
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 |
HE17H068
|
Data processing |
MAS5 signals and detection calls were generated by GCOS and scaled to 1000.
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|
|
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 |
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