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Sample GSM1247635 Query DataSets for GSM1247635
Status Public on Mar 01, 2014
Title Control Morpholino biological replicate 2
Sample type RNA
 
Source name Zebrafish embryo hearts a 3 days post-fertilization
Organism Danio rerio
Characteristics tissue: heart
age: 3 days post-fertilization
Treatment protocol Hearts were purified from 3 dpf zebrafish as described in Burns CG, MacRae CA. Purification of hearts from zebrafish embryos. Biotechniques 2006; 40:278-81; PMID:16568816. Total RNA was extracted with the Trizol method
Growth protocol Embryos were injected at the 1-cell stage and raised under standard conditions
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from tumors using Trizol reagent according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared from 5 ug total RNA using the GeneChip IVT labeling kit, according to the manufacturer's instructions (#702232 rev 2, Afymetrix, Inc., Santa Clara, CA).
 
Hybridization protocol Hybridization was carried out according to Affymetrix protocol 701027 rev 5, using Affymetrix Fluidics Station 450.
Scan protocol Arrays were scanned with the Affymetrix GeneChip Scanner 3000 using default parameters
Data processing Probeset-level normalization was achieved using the MAS5.0 algorithm. Data analysis and linear modeling were performed in the R programming language, utilizing functions from Linear Models for Microarray Data. For each probe, a moderated t-statistic (with standard errors moderated across genes) was computed using a Bayesian model. For each transcript, signal-to-noise ratios (SNR) were computed for each respective morphant compared to the control group
 
Submission date Oct 22, 2013
Last update date Mar 01, 2014
Contact name James F Amatruda
E-mail(s) james.amatruda@utsouthwestern.edu
Phone 214-648-3896
Organization name University of Texas Southwestern Medical Center
Department Pediatrics and Molecular Biology
Street address 5323 Harry Hines Boulevard
City Dallas
State/province TX
ZIP/Postal code 75390-8534
Country USA
 
Platform ID GPL1319
Series (1)
GSE51541 Autophagy is essential for cardiac morphogenesis during vertebrate development

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

Data table
ID_REF VALUE ABS_CALL
Dr.19936.1.S1_at 11.50826 P
Dr.18586.1.S1_at 52.25127 P
Dr.19011.1.A1_at 8.637054 M
Dr.179.1.S1_at 5.138463 A
Dr.179.1.S2_at 0.4475292 A
Dr.19748.1.A1_at 6.397001 A
Dr.18566.1.S1_at 11.30652 A
Dr.8231.1.S1_at 5.48397 P
Dr.18309.1.S1_at 8.412589 P
Dr.8233.1.S1_at 461.1053 P
Dr.22094.1.A1_at 127.7981 P
Dr.8234.1.S1_at 1.156357 A
Dr.8077.1.S1_at 2.020623 A
Dr.8077.2.S1_a_at 3.761771 A
Dr.224.1.S1_at 18.31463 P
Dr.9661.1.A1_at 32.86271 P
Dr.16348.1.S1_at 6.253137 A
Dr.15060.1.S1_at 131.8871 P
Dr.11417.1.A1_at 162.6434 P
Dr.4524.1.A1_at 472.0869 P

Total number of rows: 15617

Table truncated, full table size 422 Kbytes.




Supplementary file Size Download File type/resource
GSM1247635_22_control_replicate_2_1773E_RR1.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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