characteristics.text: 2024-12-24
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Deutsches Krebsforschungszentrum (DKFZ)
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS18689006
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13987:sx42_24
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Four Core Genotypes colony founders on the C57BL/6J background were obtained from The Jackson Laboratory (strain 010905). Two XYT individuals were mated with wild-type C57BL/6J (Janvier-Labs) or CAST/EiJ (bred at the German Cancer Research Center) females to respectively generate pure C57BL/6J and B6 x CAST F1 hybrid XXO, XXT, XYO and XYT progeny. Wild-type C57BL/6J males (Janvier-Labs) were imported and housed for one week prior to sacrifice. All animals were maintained as virgins (apart from the two XYT founders) and housed in groups of up to six mice in Tecniplast GM500 IVC cages with a 12 hour light/dark cycle. Mice had ad libitum access to water, food (Kliba 3437) and environmental enrichment. The colony was regularly controlled for infections using sentinel mice to ensure a healthy status. All breedings and organ collections were carried out with the approval of the Regierungspräsidium Karlsruhe. Animal genotype (i.e. XXO, XXT, XYO or XYT) was assigned based on an independent assessment of sex chromosome complement and gonadal sex. Gonadal sex was determined by visual assessment of external morphology, initially at the time of weaning and confirmed at the time of sacrifice   Whole livers were isolated from 48 individuals, snap-frozen on liquid nitrogen and pulverized with the cryoPREP® Automated Dry Pulverizer (Covaris #CP02) using the TT2 holder, TT2 consumables and impact setting. Pulverised material was stored at -80˚C. Samples were stored in aliquots of 100 µL at -80° C. Nuclei isolation was performed as described previously by Martin et al. (2022), with the following modifications: ~20mg pulverised frozen liver tissue was dounced ten times with pestle A and ten times with pestle B (Sigma #8938) in 1ml hypotonic lysis buffer solution B containing 10 mg/ml BSA (Sigma # 126609). The homogenate was then diluted 1:5 in fresh lysis buffer, incubated on ice for 10min, filtered through a 30μm CellTrics filter (Sysmex # 04-004-2326) and spun at 700 rcf for 5min. Pelleted nuclei were resuspended in 1ml SPBSTM supplemented with 1% DEPC, spun again and resuspended in 1ml SPBSTM. Nuclei were fixed by addition of 4.3ml pre-chilled fixation solution (4ml MeOH and 300ul 16.7mg/ml DTSSP, Sigma # 803200) and incubation on ice for 15min, rehydrated by addition of 3 volumes of SPBSTM, spun at 700 rcf for 10 min, resuspended in 1ml SPBSTM and stored at -80 in 250 μl aliquots. Nuclei quality and concentration was quantified using a LUNA-FX7 automated cell counter (Logos). Library preparation was performed as described previously by Martin et al. (2022), with the following modifications. Nuclei were passed through a 20μm EasyStrainer filter (Greiner # 542120) prior to distribution across the reverse transcription plate.  Following protease digestion, the optimal Tn5 concentration was empirically determined by testing a 2-fold dilution series (0.25, 0.13, 0.06, 0.03 N7-loaded Tn5 per 5ul reaction) on a small subset of wells (2 per dilution). Final libraries were subjected to a two-sided (0.45x/0.80x) AmpureXP bead cleanup but not gel extraction.
characteristics.characteristic: description
characteristics.text: XXT
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: 23
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: Testes
characteristics.characteristic: sex
characteristics.text: Four Core Genotype
characteristics.characteristic: strain
characteristics.text: sx42_24
characteristics.characteristic: title