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Sample GSM6846559 Query DataSets for GSM6846559
Status Public on Feb 23, 2024
Title Control rep4
Sample type SRA
 
Source name Colon
Organism Mus musculus
Characteristics tissue: Colon
cell line: Control
cell type: Colon
genotype: Non-induced AKP
treatment: No treatment (control)
Extracted molecule polyA RNA
Extraction protocol Cells were collected using TrypLE Express Enzyme, lysed in RLT buffer (QIAGEN, Catalog No. 74004), and the RNA was extracted using the QIAGEN RNeasy Micro Kit (QIAGEN, Catalog No. 74004) according to the manufacturer’s instructions.
Purified RNA was quality checked using a TapeStation 4200 (Agilent), and 500 ng were used for QuantSeq 3′ mRNA-Seq library construction according to the manufacturer’s instructions (Lexogen, Catalog No. 015.96).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Control rep4
Data processing Reads were aligned to the mouse genome (GRCm39) using star (version 2.7.0e).
R (version 4.1.2) was used to perform the differential expression analyses. Count values were imported and processed using edgeR.
Expression values were normalized using the trimmed mean of M values (TMM) method and lowly-expressed genes (< 1 counts per million) were filtered out.
Differentially expressed genes were identified using linear models (Limma-Voom), and P values were adjusted for multiple comparisons by applying the Benjamini-Hochberg correction method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include count values for each sample
 
Submission date Dec 16, 2022
Last update date Feb 23, 2024
Contact name L. Francisco Lorenzo-Martín
E-mail(s) luis.lorenzomartin@epfl.ch
Organization name École Polytechnique Fédérale de Lausanne (EPFL)
Lab Laboratory of Stem Cell Bioengineering
Street address EPFL – SV – IBI – LSCB – Station 15
City Lausanne
State/province Vaud
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL19057
Series (2)
GSE221159 Spatiotemporally resolved ex vivo colorectal cancer development in engineered mini-colons (RNA-Seq AKP lines)
GSE221163 Spatiotemporally resolved ex vivo colorectal cancer development in engineered mini-colons
Relations
BioSample SAMN32275724
SRA SRX18727078

Supplementary file Size Download File type/resource
GSM6846559_dR4_F19_counts.txt.gz 137.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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