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Sample GSM88013 Query DataSets for GSM88013
Status Public on Nov 09, 2006
Title PriMk_Expt1_Day9_rep1
Sample type RNA
 
Channel 1
Source name PriMk_Expt1_Day9
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 9 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 2270 33 3.70 277 38 5.12 NULL NULL
2 NULL 68 32 3.97 45 38 4.71 NULL NULL
3 NULL 122 32 3.80 83 38 4.30 NULL NULL
4 NULL 1666 32 3.57 5637 39 4.28 NULL NULL
5 NULL 312 33 3.77 386 38 5.40 NULL NULL
6 NULL 82 33 4.03 57 38 5.01 NULL NULL
7 NULL 2115 34 4.32 57 38 4.90 NULL NULL
8 NULL 429 33 4.00 886 39 4.70 NULL NULL
9 0.3506 310 33 3.66 260 39 4.39 0.4022 -0.3506
10 NULL 76 34 3.73 54 39 4.24 NULL NULL
11 NULL 92 33 3.85 74 39 4.50 NULL NULL
12 NULL 99 33 3.99 111 38 4.45 NULL NULL
13 -0.1957 79 34 4.37 63 39 4.56 0.4101 0.1957
14 NULL 2228 34 3.96 60 39 4.64 NULL NULL
15 -0.8548 707 34 4.00 1781 39 4.74 0.8237 0.8548
16 -0.0238 139 34 3.86 149 39 4.10 0.0317 0.0238
17 NULL 74 34 3.69 57 39 4.89 NULL NULL
18 0.0471 177 34 3.61 173 38 4.85 0.0682 -0.0471
20 0.7298 84 34 3.93 50 38 4.90 0.9556 -0.7298
21 NULL 2383 34 3.70 76 39 4.39 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1093 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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