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Sample GSM88007 Query DataSets for GSM88007
Status Public on Nov 09, 2006
Title PriMk_Expt1_Day3_rep1
Sample type RNA
 
Channel 1
Source name PriMk_Expt1_Day3
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 3 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 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 2048 38 4.32 357 42 4.88 NULL NULL
2 NULL 115 38 3.62 67 42 4.96 NULL NULL
3 1.0953 213 38 3.93 110 42 4.65 0.9833 -1.0953
4 -0.497 3571 38 4.12 5908 42 5.07 0.7268 0.4970
5 NULL 391 38 4.15 457 42 5.11 NULL NULL
6 NULL 135 38 4.15 84 42 4.97 NULL NULL
7 NULL 1673 39 4.03 105 42 5.22 NULL NULL
8 NULL 707 39 4.02 1144 43 5.21 NULL NULL
9 NULL 561 39 3.66 447 43 5.12 NULL NULL
10 0.2072 121 38 3.81 87 42 5.14 0.2527 -0.2072
11 0.012 146 39 4.04 112 42 4.77 0.0269 -0.0120
12 -0.1569 154 38 3.93 140 42 4.75 0.2682 0.1569
13 -0.0051 135 38 3.86 100 42 4.86 0.0114 0.0051
14 NULL 1822 38 3.83 106 42 4.70 NULL NULL
15 NULL 1271 39 4.17 2143 43 5.38 NULL NULL
16 0.1092 268 38 3.71 239 41 4.67 0.2072 -0.1092
17 -0.1315 111 38 4.19 77 43 5.01 0.2774 0.1315
18 -0.0499 307 38 3.71 320 42 4.95 0.0651 0.0499
20 1.4949 126 38 3.91 69 41 4.62 0.9799 -1.4949
21 NULL 1940 39 4.01 105 42 4.61 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1099 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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