|
| Status |
Public on Sep 05, 2013 |
| Title |
male_control_139 |
| Sample type |
RNA |
| |
|
| Source name |
male_control
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: control
gender: male
case_id: 139
age: 52
tissue: postmortem hippocampus
cirrhosis: N
smoker: Yes
post-mortem-interval (hrs): 32
brain ph at time of freezing: 6.76
labeling_batch: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol using 2 times recommended volume, followed by Qiagen RNeasy column
|
| Label |
biotin
|
| Label protocol |
WT protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay, rev. 5
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol for Gene ST type arrays
|
| Scan protocol |
Scanned using Affymetrix GCOS
|
| Description |
HE32H039
|
| Data processing |
Partek 6.3 was used to generate the RMA data, using the core probesets only option. This option generated the 'core' probesets as defined by Affymetrix as well-defined. This option generated 28,869 probe sets. Using the CEL files you may generate the rest, but these 28,869 probe sets were all that was used for the analysis. RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed. These are the standard defaults used in Partek.
|
| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
Dec 15, 2022 |
| 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 |
GPL6244 |
| Series (1) |
| GSE44456 |
Stress-response pathways are altered in the hippocampus of chronic alcoholics. |
|
