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Sample GSM9255243

Query DataSets for GSM9255243

Status

Public on Dec 14, 2025

Title

MCF7 N4

Sample type

SRA

Source name

MCF-7

Organism

Homo sapiens

Characteristics

cell line: MCF-7
cell type: epithelial cells
genotype: WT
treatment: WT on collagen

Treatment protocol

MCF7 cells were seeded on a collagen matrix (0,5mg/ml in DPBS, 4h polimerization 37°) or on collagen-matrix decorated collagen-tracks during 72h

Growth protocol

MCF7 cells were cultivated on DMEM high glucose glutamax, 10% fetal bovine serum at 37° and 5% CO2 in humidified atmosphere

Extracted molecule

total RNA

Extraction protocol

mRNAs were extracted from cultured cells using the Nucleospin RNA kit (Macherey Nagel) according to the manufacturer’s instructions. RNA quality control was perfomed by Bioanalyser
Stranded mRNA prep Ligation-Illumina on Total RNA

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq X

Description

Library name: Sample5
D1570T35

Data processing

Trim-galore 0,6,7 with cutadapt 4,1 were used for trimming, then FastQC v0,11,9 was used to assess the quality.
Reads were aligned with STAR 2,7,6a on hg38 (gencode v34)
Raw counts were used as input in DESeq2 to identify differentially expressed genes between MCF-7 cells grown in presence or not of collagen-tracks. Results were filtered based on p-value < 0.05 and a Log2FC> |1.5| for further analysis such as Gene Ontology and STRING interactome pathway analyses. Everything was done under R environment (4,2,1)
Assembly: HG38
Supplementary files format and content: Raw counts for each sample in a tab delimited table.

Submission date

Sep 23, 2025

Last update date

Dec 14, 2025

Contact name

Kevin MOREAU

E-mail(s)

kevinmoreau001@gmail.com

Organization name

CNRS

Street address

Rue Henri Becquerel – CS 90030