ATAC_sample004_Bl_PSC
Homo sapiens
Protocols: We conducted a single-centre cross-sectional study in adult patients (>18 years of age) undergoing liver transplantation (LTX) for PSC (n=19), ALD (n=16) or resection for PSC-associated cholangiocarcinoma (to which we refer as PSC early-stage due to absence of cirrhosis n=2) at the University Medical Center Hamburg-Eppendorf (UKE, Hamburg, Germany). Liver tissue and whole blood were obtained from each patient at the time of surgery. Diseases were diagnosed and treated following the guidelines of the European Association for the Study of the Liver (EASL). Clinical parameters were recorded immediately before surgery. PSC patients with earlier disease stages (PSC early, n=8) were recruited from our outpatient clinic for phenotyping and functional experiments from peripheral blood. Sex and age matched healthy blood donors (HD, n=10) were used as additional controls. All patients and donors participating in this study provided written informed consent according to the ethical guidelines of the Institutional Review Board of the medical faculty of the University of Hamburg (PV4081 & PV4898). scATAC-Seq libraries were prepared using the 10x genomics single-cell NextGEM ATAC-Seq Kit v1.1 according to manufacturer's instructions. FACS sorted naive CD4+ T cells from blood of PSC patients and healthy donors were centrifuged, cell pellets were resuspended in PBS containing 0.04% bovine serum albumin (BSA). Nuclei isolation was performed by centrifugation, cell lysis and resuspension according to the demonstrated protocol for nuclei isolation (CG000169). Nuclei were counted and processes according to the low input protocol (<40.0000 nuclei). GEM generation through the 10x Chromium Controller using the 10x V1.1 H NextGEM Chip. Droplet preparation was followed by barcoding and transposition. Emulsions were resolved and single-stranded DNA was purified using Dynabeads MyOne SILANE followed by library construction and sequencing.
ENA first public
2022-04-01
ENA last update
2022-04-01
External Id
SAMEA13856671
INSDC center alias
University Medical Center Hamburg-Eppendorf
INSDC center name
University Medical Center Hamburg-Eppendorf
INSDC first public
2022-04-01T12:11:00Z
INSDC last update
2022-04-01T12:11:00Z
INSDC status
public
Submitter Id
E-MTAB-10143:ATAC_sample004_Bl_PSC
age
62
batch
7
broker name
ArrayExpress
cell type
naive T cell
common name
human
developmental stage
adult
disease
primary sclerosing cholangitis
individual
9
organism part
blood
sample name
E-MTAB-10143:ATAC_sample004_Bl_PSC
sex
male