2025-07-18
ENA first public
ERC000011
ENA-CHECKLIST
ERIBA
INSDC center name
public
INSDC status
ERS23114354
SRA accession
E-MTAB-14809:MDA-MB-231 shFTO RP repl 1
Submitter Id
ArrayExpress
broker name
MDA-MB-231
cell_line
epithelial cell
cell_type
not collected
collection date
human
common name
Protocols: Cells were grown as usual and harvested at 80% confluency in ice cold PBS with 100 μg/ml cycloheximide. Cells were lysed in lysis buffer and lysates were treated with RNase I before ultracentrifugation over a sucrose gradient. Cytosolic ribosome fractions were collected and digested with proteinase K in the presence of 1% SDS prior to RNA isolation using TRIzol. RNA fragments were run on a denaturing urea polyacrylamide gel and correctly sized fragments were eluted and recovered by ethanol precipitation. RNA was 3’ dephosphorylated and preadenylated linkers were ligated to the fragments. Following 5’ deadenylation and RecJ exonuclase treatment, fragments were cleaned using an Oligo Clean & Concentrator kit and rRNA was depleted by substractive hybridization using streptavidin beads and biotinylated rRNA oligos. Following ethanol precipitation, samples were reverse transcribed and again ethanol precipitated prior to gel purification using urea PAGE. Fragments were circularized, recovered by ethanol precipitation and subjected to library construction PCR. Size selection was performed using nondenaturing PAGE and fragments were recovered by ethanol precipitation. Library quality was confirmed using a Bioanalyzer 2100 (Agilent) with the DNA 7500 kit (Agilent) and libraries were quantified by Qubit dsDNA BR assay (ThermoFisher).
description
adult
developmental stage
breast adenocarcinoma
disease
FTO knockdown
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
pleural effusion
metastatic site
Homo sapiens
organism
Homo sapiens
organism
breast
organism part
1
replicate
Homo sapiens
scientific_name
MDA-MB-231 shFTO RP repl 1
title