Sample 21
Mus musculus domesticus
Protocols: 6 week old wild type C57BL/6J mice of both sexes (Charles River) were gonadectomized according to standard procedures, then sacrificed by carbon thiopental overdose 5 weeks later. To partially control for time-of-day effects, tissue collection windows were kept as narrow as possible and groups were collected in alternating order. Estrous cycle stage was not assessed in females. Mice were not fasted before organ collection. Liver tissue was snap-frozen on liquid nitrogen, pulverised with a Covaris CP02 automated tissue pulverizer and stored at -80˚C as described previously (Panten et al. 2024). The whole liver was dissected out, the medial lobe removed for other purposes, and the rest of the liver snap-frozen on liquid nitrogen. Half of the mice were gonadectomised and the other half subjected to the same surgical procedure except for gonad removal (sham controls). Bcl2fastq was used to converts BCL files to paired-end .fq.gz files with PCR indexes in the header.  Nuclei were released from cryopulverised liver tissue by homogenisation with a Qiagen TissueLyser III in hypotonic lysis buffer, resuspended in Sucrose PBS Triton X-100 MgCl2 (SBPSTM) buffer, fixed with MeOH/BS3, resuspended in SPBSTM and then stored at -80°C until use. Sci-RNA-seq3 library preparation was performed in 96 well plates by reverse transcription (first index), ligation (second index), second strand synthesis, protease digestion, tagmentation and PCR (third index), bead-cleanup and quality control.
ENA first public
2026-06-11
INSDC center name
German Cancer Research Center
INSDC status
public
Submitter Id
E-MTAB-17108:Sample 21
age
12
broker name
ArrayExpress
collection date
not collected
common name
western European house mouse
developmental stage
adult
genotype
wild type genotype
geographic location (country and/or sea)
not collected
group
sham
individual
csb177_42
isolate
not applicable
organism part
liver
sample name
E-MTAB-17108:Sample 21
scientific_name
Mus musculus domesticus
sex
female
strain
C57BL/6J