2024-07-24
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA115023574
External Id
UH
INSDC center name
2023-12-13T16:31:59Z
INSDC last update
public
INSDC status
ERS17469437
SRA accession
E-MTAB-13622:S2_iO43
Submitter Id
ArrayExpress
broker name
primary cell line
cell_line
fibroblast
cell_type
not collected
collection date
house mouse
common name
Protocols: primary intestinal fibroblasts derived from Lkb1fl/fl mice were treated with either AdCre or AdGFP adenovirus and at day 4 after transduction treated with or without LPS (1ug/ml). Cells were lysed and RNA extracted after 24h. RNA from fibroblasts was isolated using the Nucleospin RNA II isolation kit (Macherey-Nagel) RNA sequencing was performed using 3′UTR RNA sequencing with a 'Pool Seq' method, which is based on the Dropseq approach for single-cell sequencing (Macosko et al., 2015). The method involves priming mRNA using an oligo-dT primer incorporating a 12 bp barcode and an 8 bp unique molecular identifier (UMI) sequence. The UMI enables the removal of PCR duplicates during data analysis. To generate double-stranded cDNA, the single-stranded cDNA was converted using the template-switch effect, followed by PCR amplification using SMART PCR primers.
description
adult
developmental stage
Peutz-Jeghers syndrome
disease
AdCre+;Lkb1fl/fl
genotype
not collected
geographic location (country and/or sea)
ED341
individual
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
intestine
organism part
Mus musculus
scientific_name
1ug/ml LPS 24h
stimulus
S2_iO43
title