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Sample GSM88012 Query DataSets for GSM88012
Status Public on Nov 09, 2006
Title PriMk_Expt1_Day7_rep1
Sample type RNA
 
Channel 1
Source name PriMk_Expt1_Day7
Organism Homo sapiens
Characteristics Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 24, Caucasian
Biomaterial provider All Cells, Berkeley, CA
Treatment protocol Cultured for 7 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) 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)
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 1727 41 5.15 146 43 5.47 NULL NULL
2 NULL 111 41 4.48 56 41 5.21 NULL NULL
3 NULL 158 42 4.94 98 41 4.32 NULL NULL
4 NULL 939 43 5.07 1647 41 4.73 NULL NULL
5 NULL 273 42 5.64 220 41 4.77 NULL NULL
6 NULL 134 42 4.76 80 42 5.01 NULL NULL
7 NULL 1661 44 5.55 80 41 4.79 NULL NULL
8 NULL 439 43 4.77 558 42 5.14 NULL NULL
9 -0.0813 240 44 4.93 209 42 4.84 0.1245 0.0813
10 NULL 102 44 5.30 70 42 5.49 NULL NULL
11 -0.3188 115 44 4.71 80 41 4.77 0.4627 0.3188
12 NULL 116 44 5.75 89 42 4.46 NULL NULL
13 0.0716 120 45 5.62 79 42 4.60 0.1103 -0.0716
14 NULL 1763 44 5.63 81 42 4.91 NULL NULL
15 -0.8064 557 44 5.42 1035 42 5.27 0.7154 0.8064
16 NULL 215 43 4.45 185 42 4.85 NULL NULL
17 NULL 98 43 5.48 58 41 4.99 NULL NULL
18 NULL 274 43 5.62 237 42 5.36 NULL NULL
20 1.0314 127 45 5.64 63 42 5.17 0.9989 -1.0314
21 NULL 1865 45 5.11 88 41 4.70 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1092 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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