NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM87962 Query DataSets for GSM87962
Status Public on Nov 09, 2006
Title CHRF_Expt3_DMSO_4d_rep1
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) [email protected]
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 732 37 3.83 525 59 7.81 NULL NULL
2 NULL 40 38 3.85 59 61 8.40 NULL NULL
3 1.5255 80 38 4.06 101 61 8.89 0.9991 -1.5255
4 NULL 1037 38 3.86 9131 61 8.68 NULL NULL
5 0.1662 204 39 3.89 751 60 8.02 0.1756 -0.1662
6 NULL 47 39 3.81 82 60 8.16 NULL NULL
7 NULL 586 39 3.94 96 61 8.74 NULL NULL
8 -0.0438 393 38 4.14 1875 60 7.98 0.0512 0.0438
9 0.0997 197 39 4.00 770 61 7.97 0.1059 -0.0997
10 NULL 47 39 4.17 83 61 8.21 NULL NULL
11 -0.2292 52 39 4.07 111 61 8.49 0.4609 0.2292
12 -1.3621 48 39 3.23 171 61 7.98 0.9997 1.3621
13 -0.0609 50 39 4.18 101 60 8.34 0.1297 0.0609
14 NULL 653 38 4.06 94 60 7.08 NULL NULL
15 NULL 568 39 4.21 4744 60 7.93 NULL NULL
16 -0.0364 73 39 4.45 248 60 8.11 0.0444 0.0364
17 NULL 45 39 3.99 75 60 8.47 NULL NULL
18 -0.2188 124 39 4.00 546 60 8.43 0.3520 0.2188
20 NULL 47 38 3.77 66 60 7.83 NULL NULL
21 NULL 741 40 3.78 103 60 8.38 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1093 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap