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Sample GSM7211145 Query DataSets for GSM7211145
Status Public on Apr 30, 2023
Title EIC_4026
Sample type SRA
 
Source name Mammary
Organism Mus musculus
Characteristics strain: FVB/N
Sex: Female
tissue: Mammary
cell line: EIC Cell line
genotype: EIC/WT
treatment: Doxycyline (10ug/mL)
Growth protocol Cells grown in 10% FBS DMEM supplemented with EGF, Insulin and pitutary extract as described in Attalla et al, 2023. Cells either maintained with Doxycycline (Dox) 10ug/mL
Extracted molecule total RNA
Extraction protocol Qiagen RNEasy Mini kit was used according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Library Prep Kit following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Adaptor sequences and low quality score bases (Phred score < 30) were trimmed using Trimmomatic (Bolger et al., 2014)
Reads were aligned to the GRCm38 mouse reference genome assembly using STAR (Dobin et al., 2012)
Read counts were obtained using HTSeq (Anders et al., 2015) with parameters -m intersection-nonempty -stranded=no
Raw counts were normalized using edgeR’s TMM algorithm (Robinson et al., 2010) and were then transformed to log2-counts per million (logCPM) using the voom function implemented in the limma R package (Ritchie et al., 2015)
To assess differences in gene expression levels between the different conditions, we fitted a linear model using limma’slmfit function(method="robust" parameter was applied for end-stage tumor dataset)
Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method
Distinct patterns of gene expression changes were identified using unsupervised hierarchical clustering method (R function hclust with Euclidean distance and complete linkage metrics)
Assembly: GrCM38/mm10
Supplementary files format and content: A tab-delimited text files includes RPKM values for all samples.
 
Submission date Apr 21, 2023
Last update date Apr 30, 2023
Contact name Sherif Samer Attalla
E-mail(s) sherif.attalla@mail.mcgill.ca
Organization name McGill
Department Goodman Cancer Institute
Lab Muller lab
Street address 1160 Ave. Pine W
City Montreal
State/province Quebec
ZIP/Postal code H3A1A3
Country Canada
 
Platform ID GPL17021
Series (1)
GSE230272 HER2∆16 Engages ENPP1 To Promote an Immune Cold Microenvironment in Breast Cancer [cell line]
Relations
BioSample SAMN34284909
SRA SRX20044844

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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