E-MTAB-6588:Sample 12
Mus musculus
Protocols: RNA was harvested by Trizol, DNA contaminations were removed by DNase1 digestion in the presence of Rnase Inhibitor, followed by RNA purification via phenol/chloroform extraction. For RNA Isolation, organoids were transferred to 15ml collection tube and washed once with ice cold PBS. RNA was extracted with Trizol, followed by DNA digestion. We established organoids from the small intestine of NICDEYFPflox/flox/p53flox/flox; VillinCreERT2 mice bred under sterile conditions. Small intestines were dissected and small intestinal crypt were isolated and cultured as 3D-intestinal organoids (as described in Sato et al. Nature 459, 262-265 (2009)). Mutagenesis were induced by 4-OHT-Tamoxifen (400nM for 24h). Further on, mutant organoids were cultured without 4-OHT-Tamoxifen and in the absence of the growth factors EGF, R-Spondin1 and Noggin. Organoids of each mouse were generated in independent experiments and cultured for more than 3 weeks prior treatment. Treatment: 1 day after seeding organoid cultures were treated with VP (Verteporfin) or MI-2 (Menin-Inhibitor2) for 24h prior sample collection. RNA was harvested by Trizol, DNA contaminations were removed by DNase1 digestion in the presence of Rnase Inhibitor, followed by RNA purification via phenol/chloroform extraction. Sequencing libraries were generated using the Illumina TruSeq Stranded mRNA Kit and sample were processed in two pools with HiSeq 4000 in one run (1 pool - 1 lane).
ENA checklist
ERC000011
INSDC center alias
MDC-Berlin
INSDC center name
MDC-Berlin
INSDC first public
2018-12-24T17:01:53Z
INSDC last update
2018-03-27T10:00:44Z
INSDC status
public
SRA accession
ERS2320804
Sample Name
ERS2320804
age
14
alias
E-MTAB-6588:Sample 12
broker name
ArrayExpress
cell type
intestinal epithelial cell
genotype
VillinCreERT2;NICD-EYFPflox/flox;p53flox/flox
growth condition
organoid culture
individual
Mouse-1
organism
Mus musculus
organism part
small intestine
phenotype
small intestinal epithelial cells with loss of p53 and expression of NICD
sex
female
stimulus
4-hydroxytamoxifen; 400 nanomolar for 24 hours
strain
C57BL/6
title
Sample 12