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Sample GSM88037 Query DataSets for GSM88037
Status Public on Nov 09, 2006
Title PriMk_Expt3_Day7_rep2
Sample type RNA
 
Channel 1
Source name PriMk_Expt3_Day7
Organism Homo sapiens
Characteristics Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 20, Caucasian, nonsmoker
Biomaterial provider All Cells, Berkeley, CA
Treatment protocol Cultured for 7 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 781 32 3.75 450 62 8.70 NULL NULL
2 NULL 50 32 3.28 71 62 9.34 NULL NULL
3 0.4992 77 32 3.11 208 64 7.85 0.7610 -0.4992
4 -0.525 2664 32 3.59 35034 66 9.11 0.5636 0.5250
5 0.2309 387 33 3.79 2127 65 9.05 0.3469 -0.2309
6 NULL 59 32 3.52 98 64 8.07 NULL NULL
7 NULL 662 32 3.47 132 63 8.06 NULL NULL
8 -0.4566 310 33 3.77 3218 64 8.02 0.6259 0.4566
9 NULL 188 33 3.64 1103 66 9.41 NULL NULL
10 -0.1667 54 32 3.59 109 65 8.80 0.8288 0.1667
11 0.1955 63 32 3.47 168 64 8.16 0.2921 -0.1955
12 -0.9409 64 33 3.91 333 64 8.76 0.9735 0.9409
13 -0.1546 59 33 3.24 140 64 8.89 0.4523 0.1546
14 NULL 705 32 3.50 108 64 8.53 NULL NULL
15 -0.6786 605 33 3.76 9241 63 8.05 0.7398 0.6786
16 -0.3389 71 33 3.75 298 64 7.87 0.6152 0.3389
17 -0.1573 56 33 3.50 137 65 8.36 0.4593 0.1573
18 0.0919 98 33 3.58 494 65 8.47 0.1311 -0.0919
20 NULL 58 34 3.75 94 65 8.97 NULL NULL
21 NULL 728 34 3.87 164 65 8.57 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1100 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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