2024-06-29
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114784727
External Id
DKFZ Heidelberg
INSDC center name
2023-12-01T14:13:18Z
INSDC last update
public
INSDC status
ERS17205839
SRA accession
E-MTAB-11602_2:AS-875888-LR-66144_ix1
Submitter Id
83
day
age
ArrayExpress
broker name
not collected
collection date
house mouse
common name
Protocols: All mice used in this study were derived from colonies maintained inhouse, at around 8 weeks of age after spermatogenesis is fully established. For the cross-species analysis, we used animals from the C57BL/6, CAST/EiJ and CAROLI/EiJ strains. For the F1 analysis, we used C57BL/6-Ly5.1 and CAST/EiJ strains as well as F1 mice derived from a C57BL/6-Ly5.1 (female) x CAST/EiJ (male) cross. scRNA-Seq of murine testicular tissue using the 10x Genomics platform was performed similarly to Ernst et al, 2019. For the cross-species dataset, single-cell suspensions were generated by enzymatic digestion using 25 mg/ml Collagenase A (Sigma, 10103578001), 25 mg/ml Dispase II (Sigma, D4693) and 2.5 mg/ml DNAse I (Sigma, 10104159001) I for 30 min at 37C. For the F1 dataset, digestion was performed using 5mg/ml Collagenase A, 5 mg/ml Dispase II and 2.5 mg/ml DNAse I. After generation of single-cell suspensions, libraries were generated using 10x library construction kits according to the manufacturers instructions. For the cross-species dataset, for each sample, 10,000 cells were loaded into one channel of the Chromium™ Single Cell A Chip (10X Genomics ®, 1000009) and scRNA-Seq libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics ®, 120237). For the F1 dataset, libraries were generated using the Chromium™ Single Cell B Chip (10X Genomics ® 1000073) and Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics ®, 1000075). After generation of single-cell suspensions, libraries were generated using 10x library construction kits according to the manufacturers instructions. For the cross-species dataset, for each sample, 10,000 cells were loaded into one channel of the Chromium™ Single Cell A Chip (10X Genomics ®, 1000009) and scRNA-Seq libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics ®, 120237). For the F1 dataset, libraries were generated using the Chromium™ Single Cell B Chip (10X Genomics ® 1000073) and Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics ®, 1000075).
description
adult
developmental stage
wild type genotype
genotype
not collected
geographic location (country and/or sea)
JP_E5_F1_rep1
individual
not applicable
isolate
DKFZ Heidelberg
laboratory
Mus musculus
organism
Mus musculus
organism
testis
organism part
Mus musculus
scientific_name
male
sex
C57BL/6-Ly5.1xCAST/EiJ
strain
AS-875888-LR-66144_ix1
title