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Sample GSM87963 Query DataSets for GSM87963
Status Public on Nov 09, 2006
Title CHRF_Expt3_DMSO_4d_rep2
Sample type RNA
 
Channel 1
Source name CHRF cells, DMSO 4d
Organism Homo sapiens
Characteristics Megakaryoblastic cell line (Witte et al., Cancer 1986; 58(2):238-44), origin male 17-month old with megakaryoblastic leukemia
Biomaterial provider R. Smith, NIH
Treatment protocol Treated with 0.02% DMSO for 4d
Growth protocol Grown in IMDM with 10% heat inactivated fetal bovine serum, 37degC, 5% CO2
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 CHRF-288 model of 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 30, 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)
GSE3838 Temporal expression profile of CHRF-288 cell line after phorbol ester stimulation
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 1321 40 4.21 503 60 8.72 NULL NULL
2 NULL 41 40 4.42 61 61 8.56 NULL NULL
3 NULL 147 41 3.96 145 61 8.03 NULL NULL
4 NULL 4718 41 4.42 16598 62 8.23 NULL NULL
5 NULL 419 41 4.33 1014 62 7.63 NULL NULL
6 NULL 50 42 4.28 79 62 8.37 NULL NULL
7 NULL 1085 43 4.33 95 62 8.75 NULL NULL
8 NULL 744 42 4.66 1980 61 8.84 NULL NULL
9 NULL 286 43 5.01 661 60 8.23 NULL NULL
10 NULL 54 43 4.46 92 59 8.03 NULL NULL
11 -0.5731 68 43 4.79 127 60 7.04 0.8084 0.5731
12 -1.6905 61 43 4.53 238 61 7.74 0.9946 1.6905
13 -0.4124 59 44 3.91 99 62 8.17 0.9503 0.4124
14 NULL 1159 43 4.03 100 61 8.22 NULL NULL
15 -0.7157 1126 44 4.02 5053 61 7.68 0.8209 0.7157
16 -0.6373 92 44 4.16 236 60 7.62 0.8933 0.6373
17 NULL 49 44 4.18 83 60 7.90 NULL NULL
18 -0.1935 168 44 4.40 435 60 8.22 0.2304 0.1935
20 NULL 49 43 3.90 70 61 8.15 NULL NULL
21 NULL 1244 43 3.86 95 59 7.65 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1106 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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