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Sample GSM87988 Query DataSets for GSM87988
Status Public on Nov 09, 2006
Title CHRF_Expt4_PMA_1d_rep1
Sample type RNA
 
Channel 1
Source name CHRF cells, PMA 1d
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 1d
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 1439 40 4.12 446 63 7.98 NULL NULL
2 NULL 54 42 4.59 69 63 8.39 NULL NULL
3 0.7141 75 41 4.26 88 63 8.69 0.9935 -0.7141
4 NULL 128 42 4.46 844 64 8.53 NULL NULL
5 0.3765 681 42 4.54 1608 64 9.33 0.3167 -0.3765
6 NULL 66 42 4.38 105 64 8.66 NULL NULL
7 NULL 1438 42 4.42 229 64 8.60 NULL NULL
8 -0.1471 905 42 4.25 3168 64 8.31 0.1168 0.1471
9 NULL 335 42 4.53 1412 64 8.40 NULL NULL
10 NULL 55 42 4.56 68 64 9.02 NULL NULL
11 0.2289 117 42 4.36 221 63 8.83 0.2870 -0.2289
12 0.0687 111 41 4.67 265 64 9.21 0.1104 -0.0687
13 0.6367 126 42 4.46 213 64 8.47 0.8017 -0.6367
14 NULL 1609 42 4.88 251 64 8.19 NULL NULL
15 -0.5887 1549 43 4.78 9413 65 8.29 0.5539 0.5887
16 0.4095 178 42 4.27 407 64 8.87 0.4567 -0.4095
17 0.4321 109 42 4.58 175 62 8.18 0.5124 -0.4321
18 -0.1911 269 42 4.15 1072 63 7.72 0.1948 0.1911
20 NULL 63 41 4.39 92 64 7.83 NULL NULL
21 NULL 1633 42 4.18 230 64 8.36 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1100 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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