2021-05-03
ENA first public
2021-04-29
ENA last update
ERC000011
ENA-CHECKLIST
SAMEA8657527
External Id
RIKEN Center for Integrative Medical Sciences
INSDC center alias
RIKEN Center for Integrative Medical Sciences
INSDC center name
2021-05-03T00:25:16Z
INSDC first public
2021-04-29T14:44:01Z
INSDC last update
public
INSDC status
ERS6342075
SRA accession
E-MTAB-10381:HDF
Submitter Id
ArrayExpress
http://www.ebi.ac.uk/efo/EFO_0009737
broker name
NHDF-Neo
cell line
fibroblast
http://purl.obolibrary.org/obo/CL_0000057
cell type
human
http://purl.obolibrary.org/obo/NCBITaxon_9606
common name
Protocols: Fibroblasts were derived from neonatal foreskin purchased (Lonza). HDF cells were iPS line iPS_HDF-f_hi6 derived in doi:10.1038/ng.2965. Bulk ATAC-seq was performed as previously described(1) with slight modifications. Briefly, 2.5×104 cells/ml were used for library preparation.1 Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr. Protoc. Mol. Biol. 109, 21.29.1-21.29.9 (2015). Due to the more resistant membrane properties of DMFB, 0.25% IGEPAL™ CA-630 (Sigma-Aldrich®) were used for cell lysis. Transposase reaction was carried out as described in the protocol followed by 10 to 12 cycles of PCR amplification. Amplified DNA fragments were purified with MinElute™ PCR Purification Kit (QIAGEN®) and size-selected with AMPure™ XP (Beckman Coulter®). All libraries were examined in Bioanalyzer™ (Agilent®) for size profiles and quantified by KAPA™ Library Quantification Kits (Kapa Biosystems®).
description
neonate
developmental stage
normal
http://purl.obolibrary.org/obo/PATO_0000461
disease
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
organism
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
organism
skin
http://purl.obolibrary.org/obo/UBERON_0000014
organism part
HDF
title