Single Cell ATAC-Seq on human cord-blood derived HSPC.

Cells from three sorted CD34+/CD38+ and three sorted CD34+/CD38-CD45RA- human cord-blood-derived HSPC samples were processed on the 10X Genomics single cell ATAC-seq platform. Additionally scATAC-Seq was performed upon human cord-blood derived GFP+/CD34+/CD38-/CD45RA- cells harbouring shCTCF and equivalently sorted cells harbouring shCtrl purified from mouse xenografts at 4 weeks post-transplantation.
Samples uploaded in bam format, aligned to hg19 with the following additional fields (as per 10x format):
CB Z Chromium cellular barcode sequence that is error-corrected and confirmed against a list of known-good barcode sequences.
CR Z Chromium cellular barcode sequence as reported by the sequencer.
CY Z Chromium cellular barcode read quality. Phred scores as reported by sequencer.
BC Z Sample index read.
QT Z Sample index read quality. Phred scores as reported by sequencer.
TR Z Adapter sequence trimmed off the end of the read.
TQ Z Base quality for the trimmed adapater sequence. Phred scores as reported by sequencer.
GP i Genome position. Note: this is an auxiliary tag used for the purpose of duplicate marking and is not intended for downstream use. We intend to deprecate this tag in subsequent versions.
MP i Genome position of mate-pair. Note: this is an auxiliary tag used for the purpose of duplicate marking and is not intended for downstream use. We intend to deprecate this tag in subsequent versions.EGA study EGAS00001004740