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Sample GSM112283 Query DataSets for GSM112283
Status Public on Aug 25, 2006
Title Donor MK09 thrombopoietin + nicotinamide Day 10 rep1
Sample type RNA
 
Channel 1
Source name Donor MK09 thrombopoietin + nicotinamide Day 10
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 6.25 mM nicotinamide added on day 5, cultured to day 10
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 1001 60 5.65 768 60 7.74 NULL
2 NULL 204 61 5.58 95 61 8.24 NULL
3 -0.2281 257 60 5.82 153 62 8.26 0.5891
4 0.7637 1119 61 5.07 8400 60 8.85 0.6564
5 0.2590 391 61 5.27 859 61 8.59 0.3184
6 NULL 225 61 5.65 149 60 9.02 NULL
7 NULL 877 62 5.17 148 60 8.27 NULL
8 0.8552 432 63 5.82 1782 62 8.58 0.9219
9 0.0907 415 62 5.12 844 61 8.40 0.1142
10 0.2123 212 64 5.17 134 60 8.07 0.6887
11 0.2232 223 64 5.32 171 60 8.03 0.5790
12 0.4243 258 64 6.00 195 59 8.17 0.8739
13 0.3020 226 65 5.80 207 61 8.04 0.2634
14 NULL 923 65 5.69 170 62 7.82 NULL
15 0.5011 801 65 6.01 4634 61 7.81 0.5884
16 0.7808 240 65 6.14 279 61 7.73 0.6155
17 NULL 214 65 6.01 123 62 8.40 NULL
18 0.5737 353 66 5.80 676 61 7.93 0.6597
20 NULL 255 66 6.23 111 61 7.83 NULL
21 NULL 973 67 6.16 166 61 8.52 NULL

Total number of rows: 22153

Table truncated, full table size 950 Kbytes.




Supplementary data files not provided

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