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Sample GSM88032 Query DataSets for GSM88032
Status Public on Nov 09, 2006
Title PriMk_Expt3_Day7_rep1
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 792 29 3.43 581 59 8.52 NULL NULL
2 NULL 41 29 3.02 66 59 7.96 NULL NULL
3 1.0083 62 28 3.12 204 59 7.85 0.9401 -1.0083
4 NULL 1472 29 3.31 49146 64 9.89 NULL NULL
5 0.3022 304 29 3.08 2790 60 8.56 0.2414 -0.3022
6 NULL 46 29 3.10 88 59 8.52 NULL NULL
7 NULL 819 29 3.23 119 59 8.02 NULL NULL
8 -0.5099 223 29 3.12 4313 60 8.65 0.3959 0.5099
9 0.155 155 29 2.96 1601 62 9.43 0.1400 -0.1550
10 0.1687 45 29 3.18 116 58 7.98 0.5578 -0.1687
11 0.2327 51 29 3.04 214 60 8.72 0.3360 -0.2327
12 -0.8276 50 29 3.35 391 61 8.20 0.9185 0.8276
13 -0.4286 44 29 2.96 154 60 9.24 0.9492 0.4286
14 NULL 889 29 3.10 157 59 8.65 NULL NULL
15 -0.6512 531 30 3.82 14692 60 8.65 0.5849 0.6512
16 -0.0113 70 30 3.72 509 59 8.07 0.0177 0.0113
17 0.2963 45 32 4.69 133 59 7.99 0.8230 -0.2963
18 0.023 96 32 3.96 804 60 7.92 0.0236 -0.0230
20 NULL 48 32 4.58 85 59 8.16 NULL NULL
21 NULL 881 32 4.82 159 60 8.24 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1090 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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