2025-09-10
ENA first public
ERC000011
ENA-CHECKLIST
Centre for Discovery Brain Sciences, University of Edinburgh
INSDC center name
public
INSDC status
ERS21102355
SRA accession
E-MTAB-14490:IP_79_80
Submitter Id
12 to 22
week
age
ArrayExpress
broker name
not collected
collection date
house mouse
common name
Protocols: Mice were culled by cervical dislocation and the brain was quickly removed and cut into 1.5 mm coronal slices using a rodent brain matrix. To obtain enough RNA, each biological sample contained PFC from two mice. Brain slices were placed in cold RNase free PBS and PFC was further dissected and collected for RNA extraction. The dissected tissue was homogenized using a dounce tissue grinder (Kimble Cat# 885303-002) in 1 mL of homogenization buffer (47 mM Tris, 94 mM KCl, 11.3 mM MgCl2, 1%NP-40, 1mM DTT, protease inhibitor (Sigma Cat# P8340), 200 U/mL of RNasin (Promega Cat# N2115), 100 μg/mL cycloheximide, 1 mg/mL heparin). The homogenate was centrifuged (10,000 g / 10’ / 4°C) to obtain a clear lysate, 10% (100 μL) of which was used to extract whole tissue RNA (Input). The remaining lysate (IP) was incubated with mouse anti HA-antibody (1:200, Biolegend Cat# 901514) for 4 hrs at 4°C in rotation, followed by addition of 200 μL of Pierce protein A/G magnetic beads (ThermoFisher Cat#88803) and incubation overnight at 4°C in rotation. The next day, beads were washed three times using high salt solution (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT and 100 μg/mL).  RNA was purified using RNeasy Plus Micro kit (Qiagen Cat# 74004). The concentration and quality of the RNA was assessed with an Agilent 2100 Bioanalyzer and only RNA samples with a concentration higher than 4 μg/μL and a RNA integrity number (RIN) greater than 7 were further sequenced.  Sequencing libraries were prepared using TruSeq RNA stranded mRNA kit (Illumina Cat# 20020594).
description
adult
developmental stage
wild type genotype
genotype
not collected
geographic location (country and/or sea)
79_80
individual
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
cerebral cortex
organism part
IP (BEC-specific)
sample type
Mus musculus
scientific_name
female
sex
PBS
stimulus
Cdh5-CRE/RiboTag
strain
IP_79_80
title