# bulk_ATACseq

ATAC-seq of human CD34+ cells retrieved from high- and low-engrafted mice.

"Molecular and phenotypic blueprint of human hematopoiesis links proliferation stress to stem cell aging"
by Emanuele Lettera, et al.

- doi: 10.1084/jem.20251805
- GEO: GSE311221


# Atac-seq analysis from xenotransplantation experiment

Reads were trimmed with Trim Galore, aligned with BWA-MEM (release 0.7.17-r1188), to the human genome (GRCh38 primary assembly). Mus musculus (GRCm39) and Bos taurus (GCF_002263795.3) genomes were used for sequential disambiguation to remove potential contaminant reads from FBS and host DNA of the in-vivo experiment. Bam files were filtered for mitochondrial, Y chromosome and PCR duplicated reads with Picard (2.25.0-0). Blacklisted regions were filtered using as reference ENCODE blacklist (hg38 v2). Soft-clipped reads were filtered out with gatk when the ratio of clipped over the total bases exceeded 0.25. Finally, only properly paired reads, with non-secondary alignment and mapping quality of at least 15 and length > 45 bp were retained. To quantify open chromatin regions, bedtools multibamcov (with parameters -q 10) was used against the Rank6 signatures regions unique of old and young conditions, generated from the previous experiment. Differential accessibility was computed with DESeq2, filtering regions with less then 10 counts, and testing for the contrast High vs Low dose (FDR 0.05). The analysis of known motif enriched in DARs was conducted with Homer software (parameters -size 200 -mask).