|
| Status |
Public on Aug 25, 2006 |
| Title |
Donor MK09 Pre-treat Day 5 rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Donor MK09 Pre-treat Day 5
|
| Organism |
Homo sapiens |
| Characteristics |
Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 21, African American
|
| Biomaterial provider |
All Cells, Berkeley, CA
|
| Treatment protocol |
Cultured 5 days
|
| Growth protocol |
Grown in X-VIVO20 serum-free media with 100 ng/mL thrombopoietin, 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 |
Primary human hematopoietic stem cell culture directed toward megakaryocytic differentiation with or without nicotinamide supplementation
|
| 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 |
Jun 02, 2006 |
| Last update date |
Aug 25, 2006 |
| 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 (1) |
| GSE4974 |
thrombopoietin-induced megakaryocyte differentiation with and without nicotinamide |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Normalized natural log (Ch2/Ch1). Replicate spots on array representing same 60mer were averaged prior to normalization. |
| 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] |
