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Sample GSM88003 Query DataSets for GSM88003
Status Public on Nov 09, 2006
Title PriMk_Expt1_Day0_rep2
Sample type RNA
 
Channel 1
Source name PriMk_Expt1_Day0
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 Uncultured
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 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) [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 (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 812 36 3.96 374 39 4.33 NULL NULL
2 NULL 83 36 3.78 45 39 4.63 NULL NULL
3 0.632 116 37 4.74 88 39 5.18 0.8000 -0.6320
4 NULL 4450 36 4.57 5675 40 4.79 NULL NULL
5 -0.0894 209 37 4.33 378 39 4.84 0.1443 0.0894
6 NULL 90 37 4.26 70 39 4.69 NULL NULL
7 NULL 697 39 4.13 85 39 4.76 NULL NULL
8 -0.2934 429 38 4.23 993 39 5.51 0.5379 0.2934
9 0.4537 327 37 4.33 421 40 4.93 0.6437 -0.4537
10 -0.0296 87 38 4.33 78 40 4.98 0.0466 0.0296
11 0.0239 105 38 4.17 99 40 4.98 0.0253 -0.0239
12 -0.2294 103 38 4.29 107 39 4.83 0.2388 0.2294
13 -0.2419 91 38 4.17 82 39 4.66 0.3666 0.2419
14 NULL 705 39 4.50 85 39 4.91 NULL NULL
15 -0.3003 683 39 4.67 1803 39 4.87 0.3849 0.3003
16 0.0885 173 38 4.24 227 38 4.41 0.1004 -0.0885
17 NULL 83 39 4.23 60 40 4.77 NULL NULL
18 0.1663 226 39 4.50 335 39 4.94 0.2648 -0.1663
20 NULL 95 39 4.28 53 39 4.68 NULL NULL
21 NULL 745 39 4.34 86 40 4.37 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1098 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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