2025-02-02
ENA first public
ERC000011
ENA-CHECKLIST
Gehring Lab Institute for Genetics  University of Cologne
INSDC center name
public
INSDC status
ERS18335245
SRA accession
E-MTAB-13839:AID_8h_A_parental
Submitter Id
ArrayExpress
broker name
HCT116
cell_line
colorectal cancer cell
cell_type
not collected
collection date
human
common name
Protocols: Cells were harvested and lysed by adding 400 µl Invitrogen™ TRIzol™ Reagent (Invitrogen; Cat# 15596018) to each well. Control, N-AID-UPF1 and C-AID-UPF1-tagged HCT116 cell lines were maintained at 37°C and 5% CO2 in a humidified incubator in McCoy's 5A (Modified) Medium (Gibco), supplemented with 10% fetal bovine serum (Gibco) and 2 mM L-glutamine (Gibco). 3x10^5 cells were seeded in 24-well plates one day before starting the depletion experiment. UPF1 depletion was induced with 500 µM indole-3-acetic acid (IAA; Sigma-Aldrich; Cat# I5148) at various time points during the experiment (between 0 and 12 hours before harvesting). All cells were harvested at the same time to minimize differences in cell numbers. Total RNA was extracted using the Direct-zol RNA MiniPrep kit (Zymo Research; Cat# R2052) including the recommended DNase I treatment according to the manufacturer's instructions. poly(A) mRNA isolation and library preparation was carried out with 600 ng RNA as input using the NEBNext Poly (A) mRNA magnetic isolation module (NEB; Cat#E7490L) and NEBNext Ultra II Directional RNA library preparation kit (NEB; Cat#E7760L) according to the manufacturer's instructions.
description
adult
developmental stage
colorectal adenocarcinoma
disease
CRISPR/Cas9
genetic modification
pSH-EFIRES-P-AtAFB2-mCherry
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
colon
organism part
1
replicate
Homo sapiens
scientific_name
male
sex
none
spike in
AID_8h_A_parental
title