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Sample GSM88025 Query DataSets for GSM88025
Status Public on Nov 09, 2006
Title PriMk_Expt2_Day9_rep2
Sample type RNA
 
Channel 1
Source name PriMk_Expt2_Day9
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 9 days
Growth protocol Cultured as described (Yang et al., Stem Cells 2002;20:320-328) with TPO, IL-3, and Flt3-ligand in serum free X-VIVO media
Extracted molecule total RNA
Extraction protocol Mk cells immunomagnetically selected using anti-CD41a-PE (Coulter; Fullerton, CA) and anti-PE magnetic beads (Miltenyi; Auburn, CA), followed by 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 megakaryocyte 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 Dec 15, 2005
Last update date Aug 24, 2007
Contact name Eleftherios Terry Papoutsakis
E-mail(s) [email protected]
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)
GSE3839 Temporal expression profile of megakaryocytic differentiation primary CD34+ cell culture
GSE8914 CHRF-288-11 and primary human megakaryocytic cell cultures provide novel insights into lineage-specific differentiation

Data table header descriptions
ID_REF
VALUE -[INV_VALUE]
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]
INV_VALUE Normalized natural log (Ch2/Ch1). Replicate spots on array representing same 60mer were averaged prior to normalization.

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 INV_VALUE
1 NULL 1443 37 3.80 619 58 8.24 NULL NULL
2 NULL 89 37 3.96 73 59 8.62 NULL NULL
3 0.4473 136 37 3.87 123 60 8.04 0.5734 -0.4473
4 -0.7774 4079 38 4.00 16540 61 8.03 0.6654 0.7774
5 0.4134 624 38 4.04 744 60 8.34 0.4509 -0.4134
6 NULL 104 38 3.71 101 60 8.58 NULL NULL
7 NULL 1340 38 3.83 132 60 8.31 NULL NULL
8 -0.4476 605 37 3.77 1651 59 8.01 0.5610 0.4476
9 0.124 443 37 3.92 694 60 8.17 0.2112 -0.1240
10 -0.453 106 37 3.91 110 60 7.46 0.7532 0.4530
11 0.0375 135 37 3.98 152 60 7.60 0.0658 -0.0375
12 -0.454 127 37 4.01 172 59 8.03 0.6831 0.4540
13 -0.5439 121 37 3.47 149 58 8.42 0.6662 0.5439
14 NULL 1437 38 3.72 126 59 7.90 NULL NULL
15 -0.6748 1114 38 3.98 4062 60 8.53 0.6849 0.6748
16 -0.3001 152 38 3.86 219 59 6.68 0.5243 0.3001
17 -0.4071 103 38 3.77 105 58 7.30 0.7021 0.4071
18 -0.0073 241 38 4.14 377 59 8.20 0.0119 0.0073
20 1.2745 119 37 3.81 86 60 7.68 0.9989 -1.2745
21 NULL 1542 38 4.11 132 60 8.10 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1105 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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