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Sample GSM137469 Query DataSets for GSM137469
Status Public on Jun 06, 2007
Title PriG_5%O2_Expt3_Day1_rep1
Sample type RNA
 
Channel 1
Source name PriG_5%O2_Expt3_Day1
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 1 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 1487 42 4.80 967 58 8.79 NULL
2 NULL 58 43 4.29 61 58 7.91 NULL
3 -0.7063 129 45 4.49 128 59 7.96 0.9150
4 0.2555 4096 44 4.48 12161 58 7.90 0.3102
5 0.2452 226 43 4.32 639 58 7.91 0.4367
6 NULL 77 44 4.54 99 58 8.45 NULL
7 NULL 1210 44 4.60 133 59 8.65 NULL
8 0.2632 483 43 4.16 1584 59 7.20 0.2954
9 -0.1446 329 43 4.17 681 58 8.04 0.2013
10 0.7034 74 44 4.34 100 58 7.95 0.9055
11 0.9246 89 45 4.47 143 59 7.39 0.9561
12 1.4832 81 44 4.24 160 59 6.85 0.9602
13 0.4818 99 44 4.23 160 59 8.57 0.7599
14 NULL 1273 44 4.62 127 59 7.46 NULL
15 0.5295 969 45 4.59 3930 59 7.50 0.5269
16 0.0242 139 44 4.58 226 57 8.20 0.0516
17 0.3418 76 45 4.42 89 57 8.12 0.5836
18 -0.1406 262 45 4.37 542 58 7.70 0.2596
20 NULL 79 44 4.72 77 59 7.82 NULL
21 NULL 1357 45 4.82 131 59 7.94 NULL

Total number of rows: 22153

Table truncated, full table size 949 Kbytes.




Supplementary data files not provided

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