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Sample GSM87997 Query DataSets for GSM87997
Status Public on Nov 09, 2006
Title CHRF_Expt4_PMA_5d_rep2
Sample type RNA
 
Channel 1
Source name CHRF cells, PMA 5d
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 10 ng/mL PMA in DMSO (0.02% final volume) for 5d
Growth protocol Grown in IMDM with 10% heat inactivated fetal bovine serum, 37degC, 5% CO2
Extracted molecule total RNA
Extraction protocol Adherent cells removed by trypsinization 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 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 1280 37 3.87 572 59 8.27 NULL NULL
2 NULL 50 38 3.97 62 59 8.48 NULL NULL
3 1.1651 129 38 3.94 148 58 7.55 0.9977 -1.1651
4 -1.0293 3117 38 3.81 31892 60 9.04 0.7618 1.0293
5 0.3557 583 38 4.07 1651 58 8.08 0.3838 -0.3557
6 NULL 71 38 3.81 103 57 8.56 NULL NULL
7 NULL 1150 39 4.10 181 57 7.77 NULL NULL
8 -0.364 509 39 4.38 2817 58 7.89 0.3592 0.3640
9 -0.2948 300 39 4.09 1291 58 7.95 0.2796 0.2948
10 -0.6211 70 39 3.69 127 59 7.90 0.6839 0.6211
11 0.095 99 39 4.13 193 58 8.04 0.1964 -0.0950
12 -1.7338 69 39 4.08 240 60 8.37 0.9997 1.7338
13 -0.3573 88 39 3.74 215 59 7.81 0.4004 0.3573
14 NULL 1168 39 4.08 205 61 8.73 NULL NULL
15 -0.3324 1388 39 4.16 8492 60 8.40 0.3232 0.3324
16 -0.2966 108 39 4.19 309 61 8.04 0.3672 0.2966
17 -0.4807 65 39 3.92 124 61 8.43 0.5622 0.4807
18 -0.3388 201 40 4.02 891 59 8.97 0.3603 0.3388
20 NULL 67 40 3.95 84 59 8.05 NULL NULL
21 NULL 486 43 7.81 224 53 13.13 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1109 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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