2024-07-29
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA113984797
External Id
Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
INSDC center name
2023-07-04T15:42:51Z
INSDC last update
public
INSDC status
ERS15968663
SRA accession
E-MTAB-12738_2:Sample 2419
Submitter Id
3
month
age
ArrayExpress
broker name
lymphocyte
cell_type
not collected
collection date
house mouse
common name
Protocols: Nuclei were isolated from frozen livers, harvested from young (3 months) and old (24 months) C57Bl/6J, Hnf4a+/0, Cebpa+/0 and Ctcf+/0 mice. Methodology to isolate and purified nuclei is described in Strzelecki et al. 2022 (JoVE, 190). Briefly, iodixanol gradient (optiprep, D1556, Sigma Aldrich Chemie) was used to purify nuclei. All nuclei were stained with Hoechst and FACS sorted according to their ploidy level into tubes containing PBS/BSA 0.05%. cDNA were made on 384-well plates using the single -nucleus-RNA-seq2 protocol based on a modified version of SMART-Seq Single Cell kit (Takara). ERCC spike-in RNA (Ambion) (0.25 μL diluted at 1:400.000) was added to the RT-Mix (5μL final reaction). After cDNA amplification, 25% of the cDNA was processed for library preparation using the standard Illumina Nextera XT. DNA Sample Preparation kit (Illumina, #FC-131-1096) and the combination of 384 Combinatorial Dual Indexes (Illumina- Set A to D, #FC-131-2001 to FC-131-2004). Final libraries were quantified and pooled for sequencing.
description
adult
developmental stage
Cebpa +/-
genotype
not collected
geographic location (country and/or sea)
CM-SNI-236(R2)-16-C
individual
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
liver
organism part
2n
ploidy
pass
post analysis well quality
Mus musculus
scientific_name
male
sex
C57BL/6J
strain
Sample 2419
title