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Sample GSM42336

Query DataSets for GSM42336

Status

Public on Jul 20, 2005

Title

temporal.txt e16.5 o-192007

Sample type

RNA

Channel 1

Source name

Mouse Universal Reference RNA

Organism

Extracted molecule

total RNA

Channel 2

Source name

e16.5 Kidney

Organism

Extracted molecule

total RNA

Description

Individual ID; o-192007
Age; 16.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Specific samples were normalized to one another: sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

Submission date

Feb 16, 2005

Last update date

Jul 20, 2005

Contact name

Darrin F Taylor

E-mail(s)

d.taylor@imb.uq.edu.au

Phone

+61 7 3346 2607

Organization name

Institute for Molecular Bioscience, Uni of Qld

Department

Genomics and Bioinformatics

Lab

Expression Genomics Lab

Street address

Research Rd

City

St Lucia

State/province

Qld

ZIP/Postal code

4072

Country

Australia

Platform ID

Series (1)

Kidney development time course

Data table header descriptions
ID_REF	ID_REF
Raw Value	Type: float; Scale: linear_scale
Control Value	Type: float; Scale: linear_scale
VALUE	log ratio (log2 of PRE_VALUE)
Flags	Type: AbsoluteCallTypeEnum; Scale: unscaled
PRE_VALUE	VALUE Type: float; Scale: log_base_e

Data table
ID_REF	Raw Value	Control Value	VALUE	Flags	PRE_VALUE
CS:02:CGEN_MOUSE_3000002_1	4.455	6.032	-0.4363543	Present	0.739
CS:03:CGEN_MOUSE_3000003_1	1.030	1.150	-0.1584293	Present	0.896
CS:04:CGEN_MOUSE_3000004_1	1.757	2.003	-0.1893513	Present	0.877
CS:05:CGEN_MOUSE_3000005_1	33.41	13.23	1.3362833	Present	2.525
CS:06:CGEN_MOUSE_3000006_1	23.16	10.08	1.2003793	Present	2.298
CS:07:CGEN_MOUSE_3000007_1	5.515	6.218	-0.1729943	Present	0.887
CS:08:CGEN_MOUSE_3000008_1	3.749	4.523	-0.2705563	Present	0.829
CS:09:CGEN_MOUSE_3000009_1	1.678	2.405	-0.5187013	Present	0.698
CS:10:CGEN_MOUSE_3000010_1	1.554	2.039	-0.3921373	Present	0.762
CS:11:CGEN_MOUSE_3000011_1	5.749	7.256	-0.3364283	Present	0.792
CS:12:CGEN_MOUSE_3000012_1	5.642	6.642	-0.2361643	Present	0.849
CS:13:CGEN_MOUSE_3000013_1	Undef	Undef		Undef
CS:14:CGEN_MOUSE_3000014_1	8.226	13.950	-0.7612133	Present	0.59
CS:15:CGEN_MOUSE_3000015_1	56.711	55.482	0.0313953	Present	1.022
CS:16:CGEN_MOUSE_3000016_1	2.351	2.208	0.0894983	Present	1.064
CS:17:CGEN_MOUSE_3000017_1	-10.11	16.3	-6.6438563	Present	0.01
CS:18:CGEN_MOUSE_3000018_1	Undef	Undef		Undef
CS:19:CGEN_MOUSE_3000019_1	8.917	8.462	0.0758753	Present	1.054
CS:20:CGEN_MOUSE_3000020_1	2.473	2.884	-0.2209503	Present	0.858
CS:21:CGEN_MOUSE_3000021_1	1.291	1.171	0.1401243	Present	1.102

Total number of rows: 22702

Table truncated, full table size 1490 Kbytes.

Supplementary data files not provided

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