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Sample GSM1611274 Query DataSets for GSM1611274
Status Public on Apr 21, 2015
Title Postnatal P12, biological rep4
Sample type RNA
 
Source name mouse trunk muscles including skeletal muscle proliferant satellite cells, P12
Organism Mus musculus
Characteristics strain/background: C57BL/6J
genotype/variation: Pax3GFP/+
tissue: trunk muscles including skeletal muscle proliferant satellite cells
age: postnatal day 12
Treatment protocol Pax3GFP/+ mice of the appropriate age were detected by PCR and splotch white tag in the belly, and GFP confirmed under fluorescent stereoscope. Muscle samples were isolated from the trunk and digested in DMEM high glucose but no phenol red, 0.1% Trypsin, 0.1% Collagenase D and 0.01mg/mL DNaseI, and purified by filtration using 100µm and 40µm cell strainers. GFP cells were stained using propidium iodide to exclude dead cells and purified via FACS Aria II based on gating of GFP signal.
Growth protocol Pax3GFP/+ mice were bred with C57BL/6J and the day where plugs were detected was considered as E0.5 (E, embryonic days).
Extracted molecule total RNA
Extraction protocol RNeasy® Micro Kit (QIAGEN) RNA extraction protocol was used according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the Encore Biotin Module (NuGEN) protocol from 100ng total RNA (http://www.nugen.com/nugen/index.cfm/support/product-resources/tech/encore-biotin-module-performance/). Single-stranded cDNA is fragmented and characterized by chemical and enzymatic methods leading to molecules of about 50 to 100 bases. Next, a biotin-labeled nucleotide is attached to the 3' end of each fragment.
 
Hybridization protocol High-density oligonucleotide arrays containing 45,000 sets of oligonucleotide probes (25 mers) that cover all 30,000 genes encoded by the murine genome (Affymetrix Mouse Genome 430 2.0 Arrays, Ref 900495) were used for gene expression detection. Hybridization during 16 hours at 45°C in a rotary oven (Affymetrix), washing and staining (GeneChip® Fluidics Station 450) and scanning (GeneChip Scanner 3000) were carried out according to NuGEN and Affymetrix protocols.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000.
Description Sample name: P-12.D.2006
Data processing Expression Console software (Affymetrix) was used for image analysis and to determine probe signal levels. The quality and statistical analysis of the data were made using the GeneSpring GX11 analysis software (Agilent Technologies).
Data needed to be pre-treated before final analysis to normalize two different sets of arrays (2006 or 2012, as indicated in the sample names).
Expression profiles were normalized in batch using the RMA algorithm (affy R package) yielding a (probe sets, samples) matrix. As the 11 samples were obtained by merging two series, the Combat algorithm (Johnson WE, et al. Biostatistics, 2007) was used to normalize the corresponding batch effect. Expression profiles were aggregated by Gene Symbol (mean across probe sets) using Affymetrix csv annotation file (na32 version).
 
Submission date Feb 13, 2015
Last update date Apr 21, 2015
Contact name Sonia Alonso-Martin
E-mail(s) alonsomartin.s@gmail.com
Phone +33684321566
Organization name Myology Research Center U974-INSERM - UPMC-Paris VI - Institut de Myologie
Department Development and stem cells
Lab Team 8 - Relaix
Street address 105 bd de l'Hôpital
City Paris
ZIP/Postal code 75013
Country France
 
Platform ID GPL1261
Series (1)
GSE65927 Early postnatal expression data from mouse skeletal muscle stem cells

Data table header descriptions
ID_REF
VALUE Data after processing by the Combat algorithm (log2)

Data table
ID_REF VALUE
1415670_at 9.85008962
1415671_at 9.308572075
1415672_at 10.11730767
1415673_at 7.040977218
1415674_a_at 8.667981422
1415675_at 8.6748278
1415676_a_at 10.73153929
1415677_at 7.859528927
1415678_at 10.06322223
1415679_at 10.4417692
1415680_at 9.298529261
1415681_at 9.148806381
1415682_at 8.090606101
1415683_at 10.40187642
1415684_at 6.890938972
1415685_at 7.713152779
1415686_at 9.693596568
1415687_a_at 9.935036513
1415688_at 9.321215051
1415689_s_at 8.641197806

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM1611274_P12_D.CEL.gz 3.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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