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Status |
Public on Apr 02, 2015 |
Title |
PBMC_1 |
Sample type |
RNA |
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Source name |
Peripheral blood monocytes
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Organism |
Homo sapiens |
Characteristics |
developmental stage: adult disease state: HIV+ cell type: Peripheral blood monocytes batch: 1 svisit: 560 date: 10/8/2011 exec07_nba: 58.8 speed07_nba: 59 wmem07_nba: 47.5 learn07_nba: 58.2 mem07_nba: 45.1 motor07_nba: 69.6 average07_nba: 56.36667 hand07_nba: 0 lastedcat: 6 age: 61 bmi: 27.9 height: 1.727 weight: 83.1 cesd: 0 race: 1 hivdate: 11/10/1991 fromscyr: 19.91 artdate: 1/15/1994 leu3n: 576 cd4low: 282 vload: 29 ml1a1: 262 total.cpe: 1 cnspengrp: 3 handd: 1 nlang: 1 smoke: 2 cnsinf: 0 hivneuro: 0 alcohol: 0 club: 0 hash: 0 cocaine: 0 heroin: 0 halluc: 0 echlor: 0 ghb: 0 anycancer: 0
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Treatment protocol |
N/A
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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
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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.
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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.
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Scan protocol |
Array chips were scanned on the iScan reader.
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Description |
Sample name: 7602346012_H
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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.
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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 |
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