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Sample GSM4818866 Query DataSets for GSM4818866
Status Public on Oct 07, 2020
Title Mut2_PAX7_E15
Sample type RNA
 
Source name myogenic stem cells
Organism Mus musculus
Characteristics tissue: myogenic stem cells
genotype/variation: SIX1/4 mutant
Treatment protocol no treatment
Growth protocol No growth protocol, the tissue is extracted directly from E15 or E18 embryos
Extracted molecule total RNA
Extraction protocol RNA extraction from Pax7-nGFP+ FACS-sorted cells was performed using the Qiagen RNeasy microkit directly after isolation. Whole back muscles required a tissue lyser lyse step in Trizol solution.
Label biotin
Label protocol 50 ng (E18.5 whole back muscles), 2 ng (E15.5 FACS-sorted cells and whole back muscles) or 0.21 ng (E18.5 FACS-sorted cells) of total RNA were reverse-transcribed following the Ovation PicoSL or PicoV2 WTA System (Nugen). Briefly, the resulting double-strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5 μg of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5 μg of Sens Target DNA were fragmented and labelled with biotin using Encore Biotin Module kit (Nugen).
 
Hybridization protocol The cDNA was then hybridized to GeneChip® Mouse Gene 1.0 or 2.0 ST (Affymetrix) at 45 °C for 17 h. After overnight hybridization, the ChIPs were washed using the fluidic station FS450 following specific protocols (Affymetrix).
Scan protocol the ChIPs were scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for quality controls
Data processing Normalisation with R, by project Project 1 : WT1_Muscle_E15,WT2_Muscle_E15,WT3_Muscle_E15,Mut1_Muscle_E15,Mut2_Muscle_E15,Mut3_Muscle_E15 → mogene20st_Mm_ENTREZG from Brainarray, version 20, Matrix 3 WT1_Muscle_E18,WT2_Muscle_E18,Mut1_Muscle_E18,Mut2_Muscle_E18 → mogene10st_Mm_ENTREZG from Brainarray, version 20, Matrix 2 Then we conserved only common genes between the two lists. Project 2 : WT1_PAX7_E15, WT2_PAX7_E15, WT3_PAX7_E15, Mut1_PAX7_E15, Mut2_PAX7_E15, Mut3_PAX7_E15, WT6_PAX7_E18, WT7_PAX7_E18, WT8_PAX7_E18, Mut6_PAX7_E18,Mut7_PAX7_E18,Mut8_PAX7_E18 mogene20st_Mm_ENTREZG from Brainarray, version 19, Matrix 1 We strictly follow the Brainrray recomandations for the normalisation by using the affy package they provide for each version of their custom CDF files.
 
Submission date Oct 06, 2020
Last update date Oct 07, 2020
Contact name Pascal Maire
E-mail(s) pascal.maire@inserm.fr
Organization name Institut Cochin. INSERM U1016, CNRS UMR 8104, U.Paris
Department Développement Reproduction et Cancer
Street address 24 Rue du Fg St Jacques
City PARIS
ZIP/Postal code 75014
Country France
 
Platform ID GPL20710
Series (1)
GSE159079 SIX1 and SIX4 homeoproteins regulate PAX7+ progenitor cell properties during fetal epaxial myogenesis

Data table header descriptions
ID_REF
VALUE log2 GC-RMA signal

Data table
ID_REF VALUE
100009600 4.40401474390484
100009609 2.27555706324773
100009614 3.37869739624888
100009664 2.92044669319881
100012 2.54592296574292
100017 5.58767620019078
100019 7.54706586223201
100033459 2.30388893942435
100034251 4.15744338202881
100034675 2.81377858160006
100034729 1.94238775944799
100034739 3.79572239513805
100034748 3.49871789600323
100036518 2.40662357178751
100036520 3.97635476165069
100036521 4.66453845765452
100036523 5.01620586910347
100036537 6.4272046476804
100036569 1.79760663241419
100036768 4.05748076216786

Total number of rows: 24973

Table truncated, full table size 576 Kbytes.




Supplementary file Size Download File type/resource
GSM4818866_5_Mut_T_15_2_MoGene-2_0-st.CEL.gz 8.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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