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Sample GSM853232 Query DataSets for GSM853232
Status Public on Dec 28, 2011
Title sphere stage zebrafish embryo_nanog-like-MO1_rep2
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 39658602_532
It is the first of second 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 292.2168
AA494792_R 1053.8406
AA494800 94.7413
AA494800_R 46.6995
AA494831 11.3142
AA494831_R 5.9486
AA494944 8.9628
AA494944_R 6.6005
AA495014 5.8396
AA495014_R 18.0201
AA495044 7.5744
AA495044_R 10.791
AA495170 67.8816
AA495170_R 63.921
AA495418 8.2084
AA495418_R 10.5021
AA497192 16.844
AA497192_R 10.2757
AA497200 114.4525
AA497200_R 591.0726

Total number of rows: 38489

Table truncated, full table size 931 Kbytes.




Supplementary file Size Download File type/resource
GSM853232.calls.gz 2.3 Mb (ftp)(http) CALLS
GSM853232.pair.gz 6.4 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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