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Sample GSM3003608 Query DataSets for GSM3003608
Status Public on Feb 15, 2018
Title 106 replicat 3 [RNA-seq]
Sample type SRA
 
Source name 106
Organism Mus musculus
Characteristics strain background: mixed
cell type: skin squamous cell carcinoma YFP positive
surface marker: CD106+, CD51-, CD61-, Epcam-
Treatment protocol KRasLSL-G12D p53fl/fl induced skin tumours. Tamoxifen was diluted at 25 mg/ml in sunflower seed oil (Sigma). Four daily intraperitoneal injection (IP) doses of 2,5 mg of TAM were administered at P28 as previously described43 to Lgr5CreER/KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ and Lgr5CreER/KrasLSL-G12D/p53fl/fl/Rosa26-DNp63-IRES-GFP.
Growth protocol Rosa26-YFP38, Lgr5CreER39, KRasLSL-G12D40and p53fl/fl41mice have been imported from the NCI mouse repository and the Jackson Laboratories.K8CreERT2 were described previously.42Pik3caH1047Rknock-in mice, in which wild-type exon 20 is replaced by H1047 mutant exon 20 upon Cre recombination, were described previously (ref. 14).Wim Declercq (Ghent University, Belgium) generated the Lgr5CreER/KrasLSL-G12D/p53fl/fl/Rosa26-DNp63-IRES-GFP mice. MMTV-PyMT female mice were kind gift of Geert Berx from Ghent University and Massimiliano Mazzone from VIB, University of Leuven. NOD/SCID/Il2Rγ null mice were purchased from Charles River.All mice used in this study were composed of males and females withmixed genetic background. No randomization and no blinding were performed in this study.Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines and with approved ethical protocols (#483N, #633N)
Extracted molecule total RNA
Extraction protocol RNA extraction from FACS isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Prior to sequencing the quality of RNA was evaluated by Bioanalyzer 2100 (Agilent). Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’srecommendations. The multiplexed libraries (11pM / 18pM) were loaded on flow cells and sequences were produced using a HiSeq PE Cluster Kit v4 and TruSeq SBS Kit v3-HS (250 cycles) on a HiSeq 1500 (Illumina). A
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description so-mm-scc5-106_ACGGACTT
Data processing Approximately 8 millions of paired-end reads of 75bp per sample for each subpopulation samples were mapped against the mouse reference genome (Grcm38/mm10) using STAR software to generate read alignments for each sample.
Annotations Grcm38.87 was obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTseq and normalized to 20 millions of aligned reads.
Average expression for each gene for the different tumour cell subpopulations was computed based on 3 biological replicates and fold changes were calculated between the subpopulations.
Genes for which all the mean expressions across the subpopulations was lower than 1 read per million of mapped reads are considered not expressed and removed for further analysis.
Genes having a fold change of expression greater or equal than 2 are considered as up-regulated and those having a fold change of expression lower or equal to 0.5 are considered down-regulated.
Genome_build: Grcm38.87
Supplementary_files_format_and_content: count files in csv contening the counts normalized per 20 millions of mapped reads for each subpopulation across all the genes
 
Submission date Feb 14, 2018
Last update date Feb 15, 2018
Contact name Cédric Blanpain
E-mail(s) cedric.blanpain@ulb.ac.be
Organization name ULB
Lab Laboratory of Stem Cells and Cancer
Street address Route de Lennik 808
City Brussels
ZIP/Postal code 1070
Country Belgium
 
Platform ID GPL18480
Series (2)
GSE110585 Identification of the tumour transition states occurring during EMT [RNA-seq]
GSE110587 Identification of the tumour transition states occurring during EMT
Relations
BioSample SAMN08535623
SRA SRX3698939

Supplementary file Size Download File type/resource
GSM3003608_106_replicat_3.csv.gz 950.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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