2025-06-01
ENA first public
ERC000011
ENA-CHECKLIST
Shenzhen Key Laboratory of Gene Regulation and Systems Biology Department of Biology School of Life Sciences Southern University of Science and Technology
INSDC center name
public
INSDC status
ERS24604448
SRA accession
E-MTAB-15131:Plate_PBMC_ATAC
Submitter Id
age
ArrayExpress
broker name
PBMC
cell line
mononuclear cell
cell type
not collected
collection date
human
common name
Protocols: Cells were cultured according to standard procedures in RPMI 1640 for K562 and GM12878 cells or DMEM for HEK293T and NIH3T3 cells, supplemented with 10% FBS (Gibco), 100 U/ml penicillin, and 100 μg/ml streptomycin sulfate. HEK293T and NIH3T3 cells were digested with 0.25% Trypsin for preparing single-cell suspension. Nuclei acid was extracted using 0.8× VAHTS DNA cleaning beads and elute in 20 μl Nuclease-free Water. For final ATAC+RNA library amplification in the plate-based workflow, 15 μl of purified pre-library was mixed with 2.5 μl RNA_plate_S5xx primer, 2.5 μl ATAC_plate_S5xx primer, 5 μl illumina P7 primer, and 25 μl Q5 High-Fidelity 2× Master Mix. PCR was performed as follows: 98 °C 1 min; 10 cycles of: 98 °C 20 s, 63 °C 20 s, 72 °C 1 min; 1 cycle of 72 °C 5 min; then hold at 10 °C. Final library was purified using 1.2× VAHTS DNA cleaning beads and elute in 20 μl Nuclease-free Water. For final ATAC library amplification in the 10x droplet workflow, 40 μl of purified 10x ATAC pre-library was mixed with 50 μl Q5 High-Fidelity 2× Master Mix, 5 µl Illumina P5 primer (10 µM), and 5 µl ATAC_droplet_N7xx primer (10 µM). PCR was performed as follows: 98 °C 1 min; 7 cycles of: 98 °C 20 s, 63 °C 20 s, 72 °C 20 s; 1 cycle of 72 °C 1 min; then hold at 10 °C. Final ATAC library was purified using 1.0× VAHTS DNA cleaning beads and elute in 20 μl Nuclease-free Water. For final RNA library amplification in the 10x droplet workflow, 40 μl of purified 10x RNA pre-libraries was mixed with 50 μl Q5 High-Fidelity 2X Master Mix, 5 µl Illumina P5 primer (10 µM), and 5 µl RNA_droplet_N7xx primer (10 µM). PCR was performed as follows: 98 °C 1 min; 7 cycles of: 98 °C 20 s, 63 °C 20 s, 72 °C 20 s; 1 cycle of 72 °C 1 min; then hold at 10 °C. Final RNA library was purified using 0.8× VAHTS DNA cleaning beads and elute in 20 μl Nuclease-free Water. These basically a combination of ATAC-seq and SHERRY protocols.
description
adult
developmental stage
wild type genotype
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
blood
organism part
Homo sapiens
scientific_name
strain
Plate_PBMC_ATAC
title