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Sample GSM1383941 Query DataSets for GSM1383941
Status Public on May 08, 2015
Title D12++
Sample type RNA
 
Source name D12++
Organism Mus musculus
Characteristics cell type: PGC
gcnf double ko: No
strain: C57BL/6
Extracted molecule total RNA
Extraction protocol 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 14h)
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.
 
Hybridization protocol Purified and labeled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina, USA) following the manufacturer’s instructions
Scan protocol After the recommended washing,the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.
Description replicate 1
Data processing The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method
 
Submission date May 09, 2014
Last update date Jan 15, 2022
Contact name Marcos J. Araúzo-Bravo
E-mail(s) mararabra@yahoo.co.uk
Phone +34 943 00 6108
Organization name Max Planck Institute for Molecular Biomedicine
Department Cell and Developmental Biology
Lab Computational Biology and Bionformatics
Street address Rogentstrasse
City Muenster
ZIP/Postal code 48149
Country Germany
 
Platform ID GPL6885
Series (1)
GSE57506 Germ cell nuclear factor regulates gametogenesis in developing gonads

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
ILMN_1212607 2.787226
ILMN_1212612 2.903391
ILMN_1212619 2.459869
ILMN_1212628 2.483714
ILMN_1212632 3.766777
ILMN_1212636 10.513157
ILMN_1212637 9.276197
ILMN_1212645 3.230155
ILMN_1212648 5.806293
ILMN_1212653 2.663198
ILMN_1212672 6.65726
ILMN_1212682 3.775774
ILMN_1212683 2.058415
ILMN_1212685 1.894278
ILMN_1212692 5.880431
ILMN_1212693 2.137695
ILMN_1212695 1.872769
ILMN_1212698 1.586953
ILMN_1212702 2.012396
ILMN_1212703 3.209583

Total number of rows: 25697

Table truncated, full table size 550 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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