NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM87968 Query DataSets for GSM87968
Status Public on Nov 09, 2006
Title CHRF_Expt3_PMA_12h_rep1
Sample type RNA
 
Channel 1
Source name CHRF cells, PMA 12h
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 12h
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 2331 45 5.52 552 59 8.01 NULL NULL
2 NULL 97 44 5.47 66 58 7.94 NULL NULL
3 NULL 175 45 9.17 147 57 7.78 NULL NULL
4 NULL 3343 43 7.46 7831 59 8.11 NULL NULL
5 NULL 448 47 8.74 517 59 8.13 NULL NULL
6 NULL 262 61 13.72 77 60 8.36 NULL NULL
7 NULL 2673 49 9.20 176 58 7.96 NULL NULL
8 NULL 866 51 11.09 1453 59 8.14 NULL NULL
9 NULL 236 55 10.59 328 59 7.90 NULL NULL
10 NULL 102 43 5.93 113 59 7.83 NULL NULL
11 NULL 123 44 6.81 153 59 8.56 NULL NULL
12 NULL 169 48 8.05 215 58 7.74 NULL NULL
13 NULL 138 47 7.83 147 58 8.40 NULL NULL
14 NULL 2824 56 24.49 167 59 8.18 NULL NULL
15 NULL 1276 48 7.83 4678 59 8.60 NULL NULL
16 -0.0296 181 42 6.17 355 58 8.15 0.0525 0.0296
17 -0.1063 74 39 4.42 106 59 8.27 0.1447 0.1063
18 -0.2046 303 40 4.48 722 59 7.75 0.3189 0.2046
20 NULL 62 38 4.49 79 59 8.50 NULL NULL
21 NULL 2727 40 7.54 175 59 8.10 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
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap