2025-10-30
ENA first public
ERC000011
ENA-CHECKLIST
Biotechnologický ústav AV ČR Institute of Biotechnology of the Czech Academy of Sciences
INSDC center name
public
INSDC status
ERS26970927
SRA accession
E-MTAB-15669:aox-D15-03
Submitter Id
ArrayExpress
broker name
4T1
cell line
4T1 AOX
cell type
not collected
collection date
house mouse
common name
Protocols: Quantitative real-time reverse transcription PCR (qRT-PCR) Total RNA was extracted from 4T1, 4T1 ρ0 and 4T1 ρ0 AOX cells in triplicates using RNAzol (Molecular Research Center), and its purity and concentration were assessed using NanoDrop (ThermoFisher Scientific). Total RNA was extracted using the Total RNA Purification Kit (NorgenBiotech, #17200) according to the manufacturer’s protocol. Total RNA was diluted in 20 μL of elution buffer (included in the kit). RNA Clean & Concentrator-5 (Zymo Research, #R1013) was used to remove contaminating genomic DNA. DNase I treatment was done following the manufacturer’s instructions (Appendix - In-column DNase I treatment). The final total RNA was diluted in 20 μL of DNase/RNase-free water (included in the kit). Concentration of total RNA was assessed using a spectrophotometer (Nanodrop 2000, ThermoFisher Scientific), and the quality of the RNA was assessed using Fragment Analyzer 5200 (Agilent, RNA 15 nt Kit, #DNF-471). The RNA quality number (RQN) was above 8 for all samples. Total RNA (100 ng) was used for the library preparation using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Lexogen, #192.24) according to the manufacturer’s protocol. Library qualities were assessed using the Fragment Analyzer 5200 (Agilent, High Sensitivity NGS Fragment Kit, #DNF-474), and concentrations were determined by the Qubit 4 Fluorometer (ThermoFisher Scientific, dsDNA Quantification Assay Kit, #Q32854). Libraries were sequenced using NextSeq500 Mid Output 150 cycles (Illumina) with 144 cycles.
description
not collected
geographic location (country and/or sea)
growth condition
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
mammary gland
organism part
3
replicate
Mus musculus
scientific_name
aox-D15-03
title