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Sample GSM88027 Query DataSets for GSM88027
Status Public on Nov 09, 2006
Title PriMk_Expt2_Day5_rep2
Sample type RNA
 
Channel 1
Source name PriMk_Expt2_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 (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 818 41 4.19 488 59 7.91 NULL NULL
2 NULL 97 40 3.91 76 60 8.08 NULL NULL
3 NULL 157 41 4.48 144 60 7.92 NULL NULL
4 NULL 4723 41 4.20 16778 60 8.01 NULL NULL
5 0.2641 490 42 3.77 946 60 8.17 0.3093 -0.2641
6 NULL 100 42 4.03 101 60 8.74 NULL NULL
7 NULL 711 42 4.19 114 60 8.16 NULL NULL
8 -0.7048 390 42 4.01 1763 59 8.11 0.7116 0.7048
9 0.5024 380 42 4.35 691 61 8.46 0.5487 -0.5024
10 NULL 99 41 4.11 103 59 8.54 NULL NULL
11 -0.4395 111 42 4.34 142 59 7.87 0.5100 0.4395
12 -1.4059 116 42 4.19 198 59 8.07 0.9049 1.4059
13 -0.4629 108 43 3.87 138 61 7.46 0.5328 0.4629
14 NULL 766 43 4.14 126 62 10.37 NULL NULL
15 -0.5325 1020 43 4.37 4826 61 8.60 0.6457 0.5325
16 -0.3803 134 43 4.37 202 61 8.56 0.4744 0.3803
17 -0.0197 100 42 4.45 107 60 7.82 0.0857 0.0197
18 -0.2752 171 43 3.96 342 60 7.99 0.4829 0.2752
20 NULL 120 43 4.63 88 60 8.19 NULL NULL
21 NULL 830 44 4.02 128 59 8.56 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1101 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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