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Sample GSM853233 Query DataSets for GSM853233
Status Public on Dec 28, 2011
Title sphere stage zebrafish embryo_nanog-like-MO1_rep3
Sample type RNA
 
Source name sphere stage zebrafish embryo_nanog-like-MO1
Organism Danio rerio
Characteristics genotype: nanog-like-MO1
phenotype: gastrulation defect
Growth protocol E3 fish water, 28°C
Extracted molecule total RNA
Extraction protocol RNA was extracted by Trizol reagent (Invitrogen).
Label Cy3
Label protocol Labeling was performed by Nimblegen using their standard protocol
 
Hybridization protocol Hybridization was performed by Nimblegen using their standard protocol
Scan protocol Scanning was performed by Nimblegen using their standard protocol
Description 39068902_532
It is the first of third nanog-like-MO1-injected biological replicates used in this experiment, each from separate cultures.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Dec 22, 2011
Last update date Dec 28, 2011
Contact name Cong Xu
E-mail(s) congxu@fas.harvard.edu
Organization name Harvard Medical School
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02134
Country USA
 
Platform ID GPL14375
Series (2)
GSE34682 Expression analysis of Nanog-like-MO1 injected zebrafish embryos at the sphere stage
GSE34684 Nanog-like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AA494792 341.6906
AA494792_R 1517.3049
AA494800 89.2868
AA494800_R 54.0461
AA494831 11.2304
AA494831_R 11.3752
AA494944 13.6523
AA494944_R 6.3297
AA495014 9.5816
AA495014_R 7.9281
AA495044 8.6589
AA495044_R 11.636
AA495170 187.2704
AA495170_R 119.8776
AA495418 8.4746
AA495418_R 9.8315
AA497192 19.7455
AA497192_R 12.8876
AA497200 116.2361
AA497200_R 533.0264

Total number of rows: 38489

Table truncated, full table size 931 Kbytes.




Supplementary file Size Download File type/resource
GSM853233.calls.gz 2.3 Mb (ftp)(http) CALLS
GSM853233.pair.gz 6.5 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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