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Sample GSM112272 Query DataSets for GSM112272
Status Public on Aug 25, 2006
Title Donor MK09 Pre-treat Day 5 rep2
Sample type RNA
 
Channel 1
Source name Donor MK09 Pre-treat Day 5
Organism Homo sapiens
Characteristics Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 21, African American
Biomaterial provider All Cells, Berkeley, CA
Treatment protocol Cultured 5 days
Growth protocol Grown in X-VIVO20 serum-free media with 100 ng/mL thrombopoietin, 37degC, 5% CO2
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 Primary human hematopoietic stem cell culture directed toward megakaryocytic differentiation with or without nicotinamide supplementation
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 Jun 02, 2006
Last update date Aug 25, 2006
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 (1)
GSE4974 thrombopoietin-induced megakaryocyte differentiation with and without nicotinamide

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 939 54 5.52 793 58 8.65 NULL
2 NULL 175 55 4.74 89 59 8.47 NULL
3 -0.4478 216 55 4.86 149 59 8.61 0.7173
4 0.7197 1103 55 4.89 10348 59 8.48 0.6511
5 0.2639 326 56 4.98 948 60 8.48 0.3137
6 NULL 177 56 5.02 132 59 7.78 NULL
7 NULL 837 57 5.26 170 59 9.19 NULL
8 0.4483 411 56 5.01 2063 61 8.39 0.5710
9 -0.1061 381 56 5.05 950 60 8.51 0.1290
10 0.1575 188 57 4.87 129 59 7.86 0.5031
11 0.4931 193 57 5.01 186 58 8.58 0.7632
12 -0.1833 225 58 5.17 192 59 7.98 0.1390
13 0.4719 189 58 5.23 189 59 7.92 0.7425
14 NULL 847 58 5.25 178 61 8.47 NULL
15 0.7383 631 57 4.99 4984 61 8.51 0.7299
16 1.1749 212 58 5.42 288 59 8.58 0.7383
17 NULL 188 57 5.22 115 60 8.45 NULL
18 0.1994 299 55 5.47 725 60 7.80 0.2515
20 -1.5591 232 60 5.22 105 58 7.62 1.0000
21 NULL 871 60 5.23 163 59 7.88 NULL

Total number of rows: 22153

Table truncated, full table size 951 Kbytes.




Supplementary data files not provided

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