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Sample GSM137473 Query DataSets for GSM137473
Status Public on Jun 06, 2007
Title PriG_5%O2_Expt3_Day5_rep1
Sample type RNA
 
Channel 1
Source name PriG_5%O2_Expt3_Day5
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 5 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]

Data table
ID_REF VALUE CH1_MEDIAN_INT CH1_MEDIAN_BKG CH1_BKG_STD_DEV CH2_MEDIAN_INT CH2_MEDIAN_BKG CH2_BKG_STD_DEV CONF_DIFF_EXPR
1 NULL 1512 42 4.35 182 59 7.60 NULL
2 NULL 92 43 4.28 69 59 8.16 NULL
3 -0.5817 148 43 3.85 108 59 8.27 0.5559
4 0.7096 2591 44 4.44 8748 60 6.76 0.5943
5 0.6413 217 43 4.00 509 60 7.93 0.8994
6 NULL 106 44 4.45 90 60 7.74 NULL
7 NULL 1541 44 4.44 83 60 8.20 NULL
8 0.7105 316 45 4.53 983 59 8.29 0.8190
9 0.3856 192 44 4.42 330 60 7.77 0.4212
10 NULL 93 44 4.27 91 60 7.98 NULL
11 0.5733 105 44 3.97 110 60 8.32 0.8463
12 0.8398 114 44 4.24 140 59 7.70 0.7763
13 NULL 105 45 4.14 92 59 8.02 NULL
14 NULL 1662 44 4.41 85 60 8.60 NULL
15 0.3165 1003 45 4.44 2828 59 7.95 0.3958
16 0.7261 133 45 4.33 134 59 8.43 0.7072
17 NULL 109 45 4.46 85 58 8.25 NULL
18 0.4780 176 45 4.51 255 60 8.35 0.6960
20 NULL 112 45 4.40 84 60 7.78 NULL
21 NULL 1738 46 4.53 110 58 8.07 NULL

Total number of rows: 22153

Table truncated, full table size 947 Kbytes.




Supplementary data files not provided

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