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Sample GSM2356833 Query DataSets for GSM2356833
Status Public on Nov 04, 2016
Title Lgr5_T5_Ctl_13
Sample type SRA
 
Source name skin squamous cell carcinoma
Organism Mus musculus
Characteristics cell type: epithelial tumor cell
genotype: Lgr5CreER/KrasG12D/p53KO/Rosa-YFP
treatment: none
Treatment protocol Epcam+ cells were plated and treated or not with TGFb during 48 hours and then FACS sorted
Growth protocol Epcam+ tumors epithelial Cells were FACS cells sorted from tumours.
Extracted molecule total RNA
Extraction protocol qiagen kit
For RNA extracted, indexed cDNA libraries were obtained using the Ovation Solo RNA-Seq Systems (NuGen) following manufacturer recommendation.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description T0 after Tgfb
Data processing Approximately 8 million of paired-end reads per sample were mapped against the mouse reference genome (GRCm38.p4/mm10) using STAR software to generate read alignments for each sample.
Annotations Mus_musculus.GRCm38.84.gtf were obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTSeq and normalized to 20 millions of aligned reads.
Fold of changes (FC) were computed on these values between the conditions.
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: tab delimited text files include count data normalized to 20 millions of aligned reads and gene informations for each sample
 
Submission date Oct 20, 2016
Last update date May 15, 2019
Contact name C├ędric Blanpain
E-mail(s) cedric.blanpain@ulb.ac.be
Organization name ULB
Street address Route de Lennik 808
City Brussels
ZIP/Postal code 1070
Country Belgium
 
Platform ID GPL18480
Series (2)
GSE71621 Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition
GSE88989 Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition [RNA-seq]
Relations
BioSample SAMN05930911
SRA SRX2255249

Supplementary file Size Download File type/resource
GSM2356833_Lgr5_T5_Ctl_13.txt.gz 916.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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