|
| Status |
Public on Apr 02, 2015 |
| Title |
PBMC_6 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood monocytes
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: adult
disease state: HIV+
cell type: Peripheral blood monocytes
batch: 1
svisit: 560
date: 11/16/2011
exec07_nba: 56.5
speed07_nba: 42.7
wmem07_nba: 34.7
learn07_nba: 38.6
mem07_nba: 48.3
motor07_nba: 38.1
average07_nba: 43.15
hand07_nba: 1
lastedcat: 5
age: 53
height: 1.803
cesd: 6
race: 1
hivdate: 5/3/1984
fromscyr: 27.54
artdate: 2/16/1992
leu3n: 688
cd4low: 262
vload: 10
ml1a1: 191
ml1a2: 253
total.cpe: 1.5
cnspengrp: 4
handd: 2
nlang: 1
smoke: 1
cnsinf: 0
hivneuro: 1
alcohol: 2
club: 0
hash: 0
cocaine: 0
heroin: 0
halluc: 0
echlor: 0
ghb: 0
anycancer: 0
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
24ml of fresh blood was collected from participants. Blood was drawn into three 8 mL Cell Preparation Tubes (CPT) containing sodium citrate. Peripheral blood mononuclear cells (PBMCs) were then isolated through centrifugation within 6 hours of collection (Salazar-Gonzalez et al., 1997). PBMCs were washed with phosphate buffered saline, and then monocytes were isolated through Rosette separation (RosetteSep®; Stem Cell Technologies) according to the manufacturer instructions). Monocytes were then pelleted, lysed, and RNA extracted using the Qiagen RNeasy kit including a DNase treatment to eliminate any potentially confounding genomic DNA contamination(Shay et al., 2003). RNA was stored at -80°C
|
| Label |
biotin
|
| Label protocol |
All total RNA samples are quanted using a Ribogreen fluorescent assay and normalized to 10 ng/ul prior to amplification. Amplified and labeled cRNA is produced using the Illumina specific Ambion TotalPrep kit. 1st and 2nd strand cDNA is produced using the Ambion kit and purified using a robotic assisted magnetic capture step. Biotinylated cRNA is produced from the cDNA template in a reverse transcription reaction. Typical yields are in excess of 1.5 ug.
|
| |
|
| Hybridization protocol |
After a second Ribogreen quant and normalization step, amplified and labeled cRNA is hybridized overnight at 58C to the expression arrays. Hybridization is followed by washing, blocking, staining (Cy3-Streptavidin) and drying on the Little Dipper processor.
|
| Scan protocol |
Array chips were scanned on the iScan reader.
|
| Description |
Sample name: 7602346063_E
|
| Data processing |
Expression data is extracted and compiled using BeadStudio software (Illumina) and extracted (un-normalized) data are reported. See 'non-normalized_data.txt' linked as supplementary file on Series record.
Illumina BeadStudio software outputs the average read intensity for beads corresponding to each probe.
|
| |
|
| Submission date |
Aug 20, 2013 |
| Last update date |
Apr 02, 2015 |
| Contact name |
Steve Horvath |
| E-mail(s) |
shorvath@altoslabs.com
|
| Organization name |
University of California, Los Angeles
|
| Department |
Human Genetics
|
| Lab |
Horvath
|
| Street address |
695 Charles E. Young Drive South, Box 708822
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE50011 |
Transcriptome analysis of HIV-infected peripheral blood monocytes |
|
