|
| Status |
Public on Oct 27, 2011 |
| Title |
HB_18_40 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Postmortem dorsolateral prefrontal cortex (DLPFC BA 46/9)
|
| Organism |
Homo sapiens |
| Characteristics |
array batch: 11
age: 60.38630137
Sex: M
race: AA
postmortem interval (pmi): 44
ph: 6.59
rna integrity number (rin): 7.9
smoking history: No
smoke at death: No
blood ethanol: Negative
highest education: 0
brain bank source: NIMH
medical examiner office: DC
surrogate variable 1 (sv1): -0.035153523
surrogate variable 2 (sv2): 0.015052614
|
| Treatment protocol |
Total RNA was extracted from dissected frozen postmortem human brain tissue.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ~ 100 mg of tissue using the RNeasy Kit (Qiagen) according to manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
500 ng of each total RNA sample or Reference is reverse transcribed with an oligo dT-T7 and amplified (T7) using the Ambion MessageAmp II Kit (Cat#1753, Ambion, Austin, TX). The generated aminoallyl UTP labeled RNAs are then coupled with either Cy3 or Cy5 mono NHS ester CyDyes from GE Healthcare, Piscataway, NJ.
|
| |
|
| Channel 2 |
| Source name |
Reference RNA pooled from all samples
|
| Organism |
Homo sapiens |
| Characteristics |
description: Reference RNA pooled from all samples
|
| Treatment protocol |
Total RNA was extracted from dissected frozen postmortem human brain tissue.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ~ 100 mg of tissue using the RNeasy Kit (Qiagen) according to manufacturer’s protocol.
|
| Label |
Cy5
|
| Label protocol |
500 ng of each total RNA sample or Reference is reverse transcribed with an oligo dT-T7 and amplified (T7) using the Ambion MessageAmp II Kit (Cat#1753, Ambion, Austin, TX). The generated aminoallyl UTP labeled RNAs are then coupled with either Cy3 or Cy5 mono NHS ester CyDyes from GE Healthcare, Piscataway, NJ.
|
| |
|
| |
| Hybridization protocol |
After purification, the labeled antisense RNAs are hybridized overnight to the oligo chips in 5X SSC, 25% Formamide and 0.2% SDS buffer at 45 oC using Maui Mixer FL hybridization chambers (BioMicro Systems, Salt Lake City, UT). The slides are then washed at room temperature in a series of SSC/SDS buffers and dried by centrifugation.
|
| Scan protocol |
A laser confocal scanner (Agilent Technologies, Palo Alto, CA) was used to scan the hybridized Cy3and Cy5 probes on the chips. The fluorescent intensities at the target locations on the array were measured using the DEARRAY software (www.scanalytics.com).
|
| Data processing |
Two color intensity data was imported, background subtracted, low intensities dropped, intensities converted to log2(sample/ref), ratios loess normalized, outliers dropped (>6 MADs), missing data from low intesity cut-off were imputed. Only the 30,176 probes (out of the total 49,152 on GPL4611) that passed all quality control and other filters were used. No "cleaning" procedure has been applied to these data - see "Overall design" and "Supplemental Files" for additional data.
|
| |
|
| Submission date |
Jun 28, 2011 |
| Last update date |
May 09, 2013 |
| Contact name |
Carlo Colantuoni |
| E-mail(s) |
ccolantu@jhmi.edu
|
| Phone |
4104931439
|
| Organization name |
Johns Hopkins Univ. School of Medicine
|
| Department |
Neurology
|
| Street address |
733 N Broadway
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL4611 |
| Series (1) |
| GSE30272 |
Temporal Dynamics and Genetic Control of Transcription in the Human Prefrontal Cortex |
|
