characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-12-31T01:13:47Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-12-31T01:13:47Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA111364030
characteristics.characteristic: External Id
characteristics.text: Center for Molecular Biology of Heidelberg  University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
characteristics.characteristic: INSDC center name
characteristics.text: 2023-12-31T01:13:47Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-12-31T01:13:47Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS13461481
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12180:SN402
characteristics.characteristic: Submitter Id
characteristics.text: 9
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Livers were dissected from adult mice, cut into small pieces and flash-frozen in a 1.5 or 2 mL Eppendorf tube in liquid nitrogen. About 30-50 mg of liver tissue was used for each experiment. Each sample was homogenized with a micropestle in 400 μl ice-cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl (pH 8), 0.1% IGEPAL, 1 μM DTT, 0.4 U/μl Murine RNase Inhibitor (New England BioLabs, cat# M0314L), and 0.2 U/μl SUPERas-In (Ambion, cat# AM2694)). The homogenates were triturated gently by a P1000 tip for 10 times, incubated on ice for 5-10 minutes and then centrifuged at 100g for 1 minute at 4 degree to pellet any unlysed tissue chunks. The supernatant was transferred into another 1.5 mL Eppendorf tube and centrifuged at 400g for 4 minutes at 4 degree to collect nuclei. The nuclei were washed twice in 400 μl homogenization buffer and strained by a 40 μm Flowmi strainer (Sigma, BAH136800040) during the second wash step to remove nuclei aggregates. The final nuclei pellet was resuspended in 30-50 μl Nuclei buffer (10X Genomics, PN-2000207). To estimate the nuclei concentration, nuclei aliquots were diluted in PBS with Hoechst and PI DNA dyes and counted on Countess II FL Automated Cell Counter (Thermo Fisher Scientific, RRID: SCR_020236). Around 15,000 nuclei were used as input for the single-nuclei RNA-seq experiment. The Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (PN-1000121, PN-1000120 and PN-1000213) were used for generating the single-nuclei RNA-seq libraries following manufacturer’s instructions. Libraries were quantified on a Qubit Fluorometer (Thermo Fisher Scientific; RRID: SCR_018095) and checked on a Fragment Analyzer (Agilent; RRID: SCR_019417) for quality control.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: MOU 9W M2 020713
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: liver
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: CD-1
characteristics.characteristic: strain
characteristics.text: SN402
characteristics.characteristic: title