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Sample GSM402356 Query DataSets for GSM402356
Status Public on May 13, 2009
Title Embryo at Day 1, male biological replicate 2
Sample type RNA
 
Source name Male
Organism Gallus gallus
Characteristics tissue: Embryo
developmental stage: Hamburger-Hamilton stage 4
sex: Male
age: 1 day
Treatment protocol Primitive streak tissues (400umx400um at 70% to 90% streak level) were dissected out using tungsten needle under dissecting microscope. Tissues were then rinsed in ice cold Tyrode's solution and transfered into the Trizol solution (GibcoBRL). Then they were frozen immediately on dry ice and stored at -80 degrees.
Growth protocol HH stage 4- chicken embryos were dissected out of eggs and put on EC culture in humidified incubator for 3 hours at 380C.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50ng total RNA.
 
Hybridization protocol Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Standard Affymetrix Scanner
Description chicken embryo at 1 day old
Data processing The data were analyzed with MAS5 data processing method implemented in Bioconductor-Affy package with 100 as target intensity.
 
Submission date May 12, 2009
Last update date May 12, 2009
Contact name Sachin Mathur
E-mail(s) sm7rf@umkc.edu
Organization name University of Missouri Kansas City
Department School of Computing & Engineering
Street address 5100 Rockhill Drive
City kansas city
State/province MO
ZIP/Postal code 64112
Country USA
 
Platform ID GPL3213
Series (1)
GSE16064 Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AB112960.CDS1.S1_at 20.90120512 A 0.398926
AF004856.CDS1.S1_s_at 19.49732378 A 0.466064
AF004857.CDS1.S1_s_at 5.135767131 A 0.80542
AF004857.CDS2.S1_s_at 8.054678666 A 0.780518
AF004857.CDS3.S1_s_at 35.84287794 A 0.466064
AF059716.CDS1.S1_at 2.605744892 A 0.665527
AF059717.CDS1.S1_at 17.41005401 A 0.72583
AF059721.CDS1.S1_at 2.218172893 A 0.850342
AF059724.CDS1.S1_at 5.006953164 A 0.870361
AF059725.CDS1.S1_at 11.27842348 A 0.533936
AF176590.CDS1.S1_s_at 29.01002161 A 0.432373
AF176591.CDS1.S1_s_at 3.290543212 A 0.633789
AF176592.CDS1.S1_s_at 18.39394434 A 0.633789
AF176592.CDS2.S1_s_at 21.19395758 A 0.665527
AF218359.CDS1.S1_at 15.11103452 A 0.601074
AF218359.CDS2.S1_at 58.63962804 A 0.111572
AF218359.CDS3.S1_at 50.40178981 A 0.171387
AF243438.CDS1.S1_s_at 21.35302233 A 0.601074
AF243438.CDS10.S1_s_at 3.363308465 A 0.780518
AF243438.CDS11.S1_s_at 19.25717817 A 0.850342

Total number of rows: 38535

Table truncated, full table size 1596 Kbytes.




Supplementary file Size Download File type/resource
GSM402356.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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