|
| Status |
Public on Nov 09, 2006 |
| Title |
CHRF_Expt3_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. |
