2025-09-29
ENA first public
ERC000011
ENA-CHECKLIST
Center for Oncological Research, Faculty of Medicine and Health Science, Antwerp University
INSDC center name
public
INSDC status
ERS21129550
SRA accession
E-MTAB-14516:CTRL_AAV_L2_CC_S11_L002
Submitter Id
ArrayExpress
broker name
Organoid of 2 cell types
cell_type
not collected
collection date
house mouse
common name
Protocols: For each of the 6 experimental groups, transcriptomic analysis was performed separately for the dissected splenium and cortex. Each group contained 5 biological replicates that were sequenced once (total of 60 sequencing datasets).  Total RNA was isolated using the RNeasy® Mini kit (Qiagen, Benelux, Belgium), according to the manufacturer’s protocol. Briefly, tissue was disrupted and lysate homogenized with lysis buffer containing b-mercaptoethanol, followed by RNA extraction and purification using RNeasy Mini spin columns. The concentration of the RNA samples was measured on the Qubit fluorometer 4.0, using the Qubit high sense RNA assay (Thermo Scientific, Wilmington, USA). The integrity and purity of the RNA samples was evaluated by the Agilent 4150 TapeStation System using the recommended RNA ScreenTape assay (Agilent Technologies, Inc., Waldbronn, Germany). For all samples, the RNA integrity number (RIN) values were above 7, indicating the superior quality of the isolated RNA.  The mRNA library preparation was performed using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt Set B1, combined with the QuantSeq-Flex First Strand Synthesis Module V2 to create longer fragments (Lexogen, Vienna, Austria). Before the library amplification PCR, the optimal PCR cycli were evaluated with the PCR Add-on and Reamplification Kit V2 (Lexogen, Vienna, Austria). The finalized cDNA libraries concentrations were measured using the Qubit high sens dsDNA kit (Qubit 4.0, Thermo Scientific, Wilmington, USA). The fragment lengths, distribution and the quality of the libraries were evaluated using the D1000 ScreenTape assay (TapeStation, Agilent Technologies, Inc., Waldbronn, Germany).
description
adult
developmental stage
AAV-eGFP
genotype
not collected
geographic location (country and/or sea)
organoid culture
growth condition
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
corpus callosum
organism part
L2
replicate
Mus musculus
scientific_name
2
sequencing label
CTRL_AAV_L2_CC_S11_L002
title