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Sample GSM87972 Query DataSets for GSM87972
Status Public on Nov 09, 2006
Title CHRF_Expt3_PMA_2d_rep1
Sample type RNA
 
Channel 1
Source name CHRF cells, PMA 2d
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 2d
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 1097 35 3.82 2361 60 7.65 NULL NULL
2 NULL 40 35 3.95 64 61 7.61 NULL NULL
3 NULL 96 36 4.18 189 59 8.13 NULL NULL
4 NULL 3028 36 4.00 21606 61 7.74 NULL NULL
5 NULL 435 37 3.97 1546 61 8.76 NULL NULL
6 NULL 53 37 4.08 110 61 8.15 NULL NULL
7 NULL 629 38 3.81 191 61 7.89 NULL NULL
8 NULL 775 38 4.04 3371 62 7.41 NULL NULL
9 NULL 281 38 3.99 1665 61 8.29 NULL NULL
10 NULL 57 37 4.09 143 60 7.59 NULL NULL
11 NULL 77 38 4.06 252 61 8.80 NULL NULL
12 NULL 57 37 3.83 405 60 8.97 NULL NULL
13 NULL 63 37 3.90 196 61 8.70 NULL NULL
14 NULL 699 37 4.20 215 60 8.13 NULL NULL
15 NULL 1027 37 4.30 8968 61 8.41 NULL NULL
16 NULL 110 37 3.72 484 60 8.78 NULL NULL
17 NULL 48 37 4.04 123 61 8.85 NULL NULL
18 NULL 240 37 4.36 1364 60 8.01 NULL NULL
20 NULL 49 38 3.91 84 60 7.84 NULL NULL
21 NULL 719 38 3.85 191 61 8.66 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1101 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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