Published July 22, 2024
| Version 0.0.2
Dataset
Open
spermatogenesis across mammals - Ensembl Release 112 mapping
Description
This repo contains remapped single-cell Anndata (h5ad) objects from the original publication "The molecular evolution of spermatogenesis across mammals (Florent Murat, Noe Mbengue et al 2023; https://doi.org/10.1038/s41586-022-05547-7)". Data was (pseudo-)remapped against Ensembl Release 112 genomes and annotations with kb-python (v0.28.2). For Macaca mulatta the NCBI GCF_003339765.1_Mmul_10_genomic.fna and GCF_003339765.1_Mmul_10_genomic.gtf was used due to low protein number in Ensembl Release 112 file Macaca_mulatta.Mmul_10.pep.all.fa.gz. Only filtered counts are provided.
If you use this data, please cite Murat and Mbengue et al. 2023.
Series information
| organism | name | sample | age | chemistry | source | genome | gtf |
| bonobo | Pan paniscus | SN219 | 36yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700457[accn] | Pan_paniscus.panpan1.1.dna.toplevel.fa.gz | Pan_paniscus.panpan1.1.112.gtf.gz |
| bonobo | Pan paniscus | SN224 | 15yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700458[accn] | Pan_paniscus.panpan1.1.dna.toplevel.fa.gz | Pan_paniscus.panpan1.1.112.gtf.gz |
| chicken | Gallus gallus | SN264 | adult | v3 | https://www.ncbi.nlm.nih.gov/sra/ERX6700407[accn] | Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna.toplevel.fa.gz | Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.112.gtf.gz |
| chicken | Gallus gallus | SN265 | adult | v3 | https://www.ncbi.nlm.nih.gov/sra/ERX6700408[accn] | Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna.toplevel.fa.gz | Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.112.gtf.gz |
| chimp | Pan troglodytes | SN074 | 45yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700425[accn] | Pan_troglodytes.Pan_tro_3.0.dna.toplevel.fa.gz | Pan_troglodytes.Pan_tro_3.0.112.gtf.gz |
| chimp | Pan troglodytes | SN112 | 14yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700426[accn] | Pan_troglodytes.Pan_tro_3.0.dna.toplevel.fa.gz | Pan_troglodytes.Pan_tro_3.0.112.gtf.gz |
| chimp | Pan troglodytes | SN193 | 21yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700427[accn] | Pan_troglodytes.Pan_tro_3.0.dna.toplevel.fa.gz | Pan_troglodytes.Pan_tro_3.0.112.gtf.gz |
| gibbon | Nomascus leucogenys | SN181 | 5yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700418[accn] | Nomascus_leucogenys.Nleu_3.0.dna.toplevel.fa.gz | Nomascus_leucogenys.Nleu_3.0.112.gtf.gz |
| gibbon | Nomascus leucogenys | SN194 | 5yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700419[accn] | Nomascus_leucogenys.Nleu_3.0.dna.toplevel.fa.gz | Nomascus_leucogenys.Nleu_3.0.112.gtf.gz |
| gorilla | Gorilla gorilla | SN180 | 43yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700420[accn] | Gorilla_gorilla.gorGor4.dna.toplevel.fa.gz | Gorilla_gorilla.gorGor4.112.gtf.gz |
| gorilla | Gorilla gorilla | SN223 | 51yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700421[accn] | Gorilla_gorilla.gorGor4.dna.toplevel.fa.gz | Gorilla_gorilla.gorGor4.112.gtf.gz |
| human | Homo sapiens | SN007 | 32yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700428[accn] | Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz | Homo_sapiens.GRCh38.112.gtf.gz |
| human | Homo sapiens | SN011 | 32yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700429[accn] | Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz | Homo_sapiens.GRCh38.112.gtf.gz |
| human | Homo sapiens | SN052 | 32yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700430[accn] | Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz | Homo_sapiens.GRCh38.112.gtf.gz |
| human | Homo sapiens | SN111 | 28yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700431[accn] | Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz | Homo_sapiens.GRCh38.112.gtf.gz |
| human | Homo sapiens | SN142 | 28yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700432[accn] | Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz | Homo_sapiens.GRCh38.112.gtf.gz |
| macaque | Macaca mulatta | SN116 | 7yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700422[accn] | GCF_003339765.1_Mmul_10_genomic.fna.gz | GCF_003339765.1_Mmul_10_genomic.gtf.gz |
| macaque | Macaca mulatta | SN143 | 9yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700423[accn] | GCF_003339765.1_Mmul_10_genomic.fna.gz | GCF_003339765.1_Mmul_10_genomic.gtf.gz |
| marmoset | Callithrix jacchus | SN117 | 10yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700543[accn] | Callithrix_jacchus.mCalJac1.pat.X.dna.toplevel.fa.gz | Callithrix_jacchus.mCalJac1.pat.X.112.gtf.gz |
| marmoset | Callithrix jacchus | SN130 | 10yo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700544[accn] | Callithrix_jacchus.mCalJac1.pat.X.dna.toplevel.fa.gz | Callithrix_jacchus.mCalJac1.pat.X.112.gtf.gz |
| mouse | Mus musculus | SN090 | 9wo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700409[accn] | Mus_musculus.GRCm39.dna.primary_assembly.fa.gz | Mus_musculus.GRCm39.112.gtf.gz |
| mouse | Mus musculus | SN115 | 9wo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700410[accn] | Mus_musculus.GRCm39.dna.primary_assembly.fa.gz | Mus_musculus.GRCm39.112.gtf.gz |
| opossum | Monodelphis domestica | SN067 | adult | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700414[accn] | Monodelphis_domestica.ASM229v1.dna.toplevel.fa.gz | Monodelphis_domestica.ASM229v1.112.gtf.gz |
| opossum | Monodelphis domestica | SN071 | 15.5mo | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700415[accn] | Monodelphis_domestica.ASM229v1.dna.toplevel.fa.gz | Monodelphis_domestica.ASM229v1.112.gtf.gz |
| opossum | Monodelphis domestica | SN277 | adult | v2 | https://www.ncbi.nlm.nih.gov/sra/ERX6700416[accn] | Monodelphis_domestica.ASM229v1.dna.toplevel.fa.gz | Monodelphis_domestica.ASM229v1.112.gtf.gz |
| platypus | Ornithorhynchus anatinus | SN253 | adult | v3 | https://www.ncbi.nlm.nih.gov/sra/ERX6700411[accn] | Ornithorhynchus_anatinus.mOrnAna1.p.v1.dna.toplevel.fa.gz | Ornithorhynchus_anatinus.mOrnAna1.p.v1.112.gtf.gz |
| platypus | Ornithorhynchus anatinus | SN260 | adult | v3 | https://www.ncbi.nlm.nih.gov/sra/ERX6700412[accn] | Ornithorhynchus_anatinus.mOrnAna1.p.v1.dna.toplevel.fa.gz | Ornithorhynchus_anatinus.mOrnAna1.p.v1.112.gtf.gz |
Methods
Extract fastq:
fastq-dump --split-files ERRXXX
Create index (kb_python 0.28.2):
kb ref -i organism.idx -g organism.t2g.txt -f1 organism.cdna.fa organism.genome.fa organism.gtf
Get counts (kb_python 0.28.2):
kb count -i organism.idx -g organism.t2g.txt -x 10XV2/10XV3 --h5ad --filter bustools ERRXXX_2.fastq ERRXXX_3.fastq
Files
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Additional details
Related works
- References
- Publication: 10.1038/s41586-022-05547-7 (DOI)
Dates
- Created
-
2024-07-17
References
- Murat, Florent, et al. "The molecular evolution of spermatogenesis across mammals." Nature 613.7943 (2023): 308-316.