|
Status |
Public on Feb 23, 2024 |
Title |
Control rep1 |
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 rep1
|
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 |
SAMN32275727 |
SRA |
SRX18727075 |