Single cell analysis of transposable elements in human testis. FASTQ files from three single-cell studies were downloaded and aligned to reference transcriptome using CellRanger. BAM files were processed by scTE to quantify transposable element expression. scTE outputs h5ad files which were analysed using scanpy. Associated presentation
- scTE: An algorithm that quantifies TE expression in single-cell sequence data
- Inputs: (1) Aligned sequence reads (BAM/SAM format). (2) The genomic location of TEs (BED format). (3) The genomic location of genes (GTF format)
- Human Genome annotations:
$ ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz
$ http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz
Also read soloTE
- GSE112013 (Guo et al, 2018) : Available here
- GSE153947 (Di Persio et al, 2021): Available here
- GSE154535 (Alfano et al, 2021) : Available here
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He, J., Babarinde, I.A., Sun, L. et al. Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE. Nat Commun 12, 1456 (2021). Read here
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Guo J, Grow EJ, Mlcochova H, Maher GJ et al. The adult human testis transcriptional cell atlas. Cell Res 2018 Dec;28(12):1141-1157. PMID: 30315278 Read here
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Di Persio S, Tekath T, Siebert-Kuss LM, Cremers JF et al. Single-cell RNA-seq unravels alterations of the human spermatogonial stem cell compartment in patients with impaired spermatogenesis. Cell Rep Med 2021 Sep 21;2(9):100395. PMID: 34622232 Read here
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Alfano M, Tascini AS, Pederzoli F, Locatelli I et al. Aging, inflammation and DNA damage in the somatic testicular niche with idiopathic germ cell aplasia. Nat Commun 2021 Sep 1;12(1):5205. PMID: 34471128 Read here