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Sample GSM112285 Query DataSets for GSM112285
Status Public on Aug 25, 2006
Title Donor MK11 Pre-treat Day 5 rep1
Sample type RNA
 
Channel 1
Source name Donor MK11 Pre-treat Day 5
Organism Homo sapiens
Characteristics Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, female donor, age 19, 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) [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 (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 1061 27 3.02 569 57 7.99 NULL
2 NULL 32 27 2.96 57 56 7.71 NULL
3 NULL 77 27 3.18 122 56 8.39 NULL
4 NULL 2283 27 3.11 10636 58 9.95 NULL
5 NULL 246 27 3.05 734 57 9.04 NULL
6 NULL 38 26 3.09 82 56 7.85 NULL
7 NULL 892 27 2.80 100 56 7.96 NULL
8 NULL 365 27 2.96 1781 56 7.92 NULL
9 NULL 305 27 2.88 576 56 7.62 NULL
10 NULL 38 27 2.61 85 56 8.57 NULL
11 NULL 49 27 3.02 119 57 7.79 NULL
12 NULL 43 26 3.14 163 54 7.91 NULL
13 NULL 43 27 3.03 101 54 7.62 NULL
14 NULL 953 27 3.25 105 56 7.96 NULL
15 NULL 696 27 3.23 3856 58 8.65 NULL
16 -0.2260 90 28 3.23 238 57 7.90 0.3050
17 -0.2263 38 28 3.35 86 57 8.01 0.5145
18 NULL 126 27 3.03 511 55 8.06 NULL
20 NULL 37 27 2.88 71 56 8.54 NULL
21 NULL 1035 27 3.06 100 57 8.21 NULL

Total number of rows: 22153

Table truncated, full table size 935 Kbytes.




Supplementary data files not provided
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