NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88022 Query DataSets for GSM88022
Status Public on Nov 09, 2006
Title PriMk_Expt2_Day12_rep1
Sample type RNA
 
Channel 1
Source name PriMk_Expt2_Day12
Organism Homo sapiens
Characteristics Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, female donor, age 21, Caucasian, nonsmoker
Biomaterial provider All Cells, Berkeley, CA
Treatment protocol Cultured for 12 days
Growth protocol Cultured as described (Yang et al., Stem Cells 2002;20:320-328) with TPO, IL-3, and Flt3-ligand in serum free X-VIVO media
Extracted molecule total RNA
Extraction protocol Mk cells immunomagnetically selected using anti-CD41a-PE (Coulter; Fullerton, CA) and anti-PE magnetic beads (Miltenyi; Auburn, CA), 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 Study of in vitro 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 24, 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)
GSE3839 Temporal expression profile of megakaryocytic differentiation primary CD34+ cell culture
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 955 35 3.81 150 60 8.10 NULL NULL
2 NULL 59 35 4.10 63 60 7.97 NULL NULL
3 NULL 89 36 4.14 82 59 8.90 NULL NULL
4 NULL 975 35 3.98 2754 59 8.42 NULL NULL
5 NULL 241 36 3.83 221 59 8.89 NULL NULL
6 NULL 68 36 4.30 72 59 7.97 NULL NULL
7 NULL 944 36 4.24 74 60 8.22 NULL NULL
8 -0.9218 211 36 3.75 494 61 7.33 0.7744 0.9218
9 0.1268 186 36 4.01 197 60 8.08 0.1556 -0.1268
10 NULL 65 36 3.79 76 60 8.30 NULL NULL
11 NULL 75 36 4.04 84 59 7.68 NULL NULL
12 -0.6043 74 36 4.55 93 60 7.71 0.9240 0.6043
13 NULL 69 37 4.13 85 59 7.78 NULL NULL
14 NULL 1089 37 4.09 75 60 7.55 NULL NULL
15 -0.8747 408 37 4.18 1043 60 8.47 0.7946 0.8747
16 NULL 82 36 3.93 104 60 8.48 NULL NULL
17 NULL 68 36 3.84 69 59 8.17 NULL NULL
18 -0.8186 93 36 3.94 117 57 8.07 0.8826 0.8186
20 NULL 75 36 4.05 67 59 7.96 NULL NULL
21 NULL 1076 37 4.09 75 59 7.33 NULL NULL

Total number of rows: 22153

Table truncated, full table size 1078 Kbytes.




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