|
Status |
Public on Jun 06, 2007 |
Title |
PriG_5%O2_Expt3_Day3_rep1 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
PriG_5%O2_Expt3_Day3
|
Organism |
Homo sapiens |
Characteristics |
Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, female donor, age 21, Caucasian, nonsmoker
|
Biomaterial provider |
All Cells, Berkeley, CA
|
Treatment protocol |
Cultured for 3 days
|
Growth protocol |
Cultured as described (Hevehan et al., Experimental Hematology 2000;28:267-75) with IL-3, IL-6, SCF and G-CSF in serum-containing McCoy's 5A media at pH 7.2 and 5% O2
|
Extracted molecule |
total RNA |
Extraction protocol |
Agilent RNA isolation mini-kit
|
Label |
Cy3
|
Label protocol |
Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)
|
|
|
Channel 2 |
Source name |
Universal Reference RNA
|
Organism |
Homo sapiens |
Characteristics |
Pooled RNA from 10 human cell lines
|
Biomaterial provider |
Stratagene
|
Extracted molecule |
total RNA |
Label |
Cy5
|
Label protocol |
Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)
|
|
|
|
Hybridization protocol |
Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying
|
Scan protocol |
Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution
|
Description |
Study of in vitro granulocyte differentiation
|
Data processing |
Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)
|
|
|
Submission date |
Sep 26, 2006 |
Last update date |
Jun 06, 2007 |
Contact name |
Eleftherios Terry Papoutsakis |
E-mail(s) |
papoutsakis@dbi.udel.edu
|
Organization name |
University of Delaware
|
Department |
Chemical Engineering
|
Street address |
15 Innovation Way
|
City |
Newark |
State/province |
DE |
ZIP/Postal code |
19711 |
Country |
USA |
|
|
Platform ID |
GPL887 |
Series (2) |
GSE5918 |
Temporal expression profile of granulocytic differentiation of primary CD34+ cells cultured under 5% O2 levels |
GSE5922 |
Temporal expression profile of granulocytic differentiation of primary CD34+ cells cultured under 5% and 20% O2 levels |
|
Data table header descriptions |
ID_REF |
|
VALUE |
Normalized natural log (Ch2/Ch1). Replicate spots on array representing same 60mer were averaged prior to normalization. |
CH1_MEDIAN_INT |
Channel 1 median intensity |
CH1_MEDIAN_BKG |
Channel 1 median background intensity |
CH1_BKG_STD_DEV |
Channel 1 background intensity standard deviation |
CH2_MEDIAN_INT |
Channel 2 median intensity |
CH2_MEDIAN_BKG |
Channel 2 median background intensity |
CH2_BKG_STD_DEV |
Channel 2 background intensity standard deviation |
CONF_DIFF_EXPR |
Confidence of differential expression (Ch1 vs Ch2, per method of Yang et al., PNAS 2003; 100:1122-1127 [0,1] |