|
| Status |
Public on Oct 22, 2014 |
| Title |
F_Control_5_None |
| Sample type |
RNA |
| |
|
| Source name |
LCLs from non-alcoholic_no treatment
|
| Organism |
Homo sapiens |
| Characteristics |
source subject id: 5
subject status: non-alcoholic (control)
subject gender: female
cell line: lymphoblastoid cell line (LCL)
treated with: none (untreated control)
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 |
HE17H045
|
| 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 |
|
