DOI: 10.5281/zenodo.12792984
title: 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.
description: 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
description: 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