2025-09-16
ENA first public
ERC000011
ENA-CHECKLIST
National Institute of Chemistry
INSDC center name
public
INSDC status
ERS22946776
SRA accession
E-MTAB-14762:dPSCs_OOPS_2
Submitter Id
ArrayExpress
broker name
embryonic cell line
cell_line
mouse embryonic stem cell
cell_type
not collected
collection date
house mouse
common name
Protocols: For control and semi-extractability samples: naive pluripotent stem cells (nPSCs), primed (pPSCs) and 1-day Wnt-differentiated cells (dPSC) were washed twice with PBS, then lysed by adding TRIzol to the plate and scraping the cells off. The samples were snap frozen on dry ice and stored at -80°C prior isolation. For OOPS, one confluent 10 cm plate was used per replicate, washed twice with ice-cold PBS before crosslinking them at 400 mJ/cm2 (UV 254 nm). After removing residual PBS, 1 mL TRIzol-LS was added to the plate before scraping off the cells content and transferring it to a 1.5 mL Eppendorf tube that was stored at -80°C.  Naive mESC (nPSCs) were grown in 2i conditions (PMID: 18497825), primed (pPSCs) in N2B27 basal medium supplemented with ActA 20 ng/ml, bFGF 12 ng/mL, IWP2 2 µM, and dPSCs were acquired from pPSCs, by switching the medium to N2B27 basal medium supplemented with ActA 20 ng/mL, bFGF 12 ng/mL, Wnt3a 250 ng/mL for 24 hours before collecting them.  For control: TRIzol samples were thawed and RNA was extracted from the aqueous phase, following manufacturer's instructions.  For semi: TRIzol samples were thawed and heated for 10 min at 55°C and also passed 40 times through a 20G needle (PMID: 28404604).  For OOPS: RNA was isolated from the interphase following published protocol (PMID: 30607034, PMID: 32651564).  Libraries for sequencing were prepared using CORALL Total RNA-Seq with RiboCop rRNA depletion verion 1 (Lexogen) with 500 ng DNase-treated RNA as input.
description
mouse embryo stage
developmental stage
normal
disease
wild type genotype
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
OOPS
rna isolation process
Mus musculus
scientific_name
dPSCs_OOPS_2
title