2024-08-28
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114349358
External Id
Department of Biological Sciences, The University of Texas at Dallas
INSDC center name
2023-09-11T18:24:28Z
INSDC last update
public
INSDC status
ERS16338402
SRA accession
E-MTAB-13339:AI_3
Submitter Id
ArrayExpress
broker name
GM12878
cell_line
B lymphoblastoid
cell_type
not collected
collection date
human
common name
Protocols: At the end of 24 hours, cells death was measured with PE Annexin-V (BD Biosciences) according to manufacturer’s instructions. Cells were stained with 7-AAD viability staining solution (BD Biosciences) and 60,000 live cells per condition were sorted by BDAria Fusion and FlowJo software. GM12878 cells were cultured with RPMI media supplemented with 10% FBS 37C with 5% CO2 When cells are 80% confluent, 1 uM of aphidicolin was added to the media and incubated for 12 hours at 37C. Sendai Virus or media was added to the media and incubated for and additional of 12 hours at 37C. Protocol was taken from different studies (Buenrostro, Giresi et al. 2013, Buenrostro, Wu et al. 2015, Corces, Trevino et al. 2017, Brunton, Garner et al. 2020) and solutions were prepared according to (Corces, Trevino et al. 2017). Briefly, 60K cells were sorted and lysed in 50 μL cold lysis buffer on ice for 3 min. Lysis was quenched by adding 1 mL of wash buffer. Cells were centrifuged at 500xg for 10 min at 4 °C and supernatant (cytoplasm) was discarded. Nuclei were gently resuspended with transposition mix and incubated at 37 °C for 30 minutes at 1,000 rpm. DNA was purified using DNA Clean & Concentrator-5 (Zymo Research, D4013) according to the manufacturer’s instructions. Protocol was taken from different studies (Buenrostro, Giresi et al. 2013, Buenrostro, Wu et al. 2015, Corces, Trevino et al. 2017, Brunton, Garner et al. 2020) and solutions were prepared according to (Corces, Trevino et al. 2017). Briefly, 60K cells were sorted and lysed in 50 μL cold lysis buffer on ice for 3 min. Lysis was quenched by adding 1 mL of wash buffer. Cells were centrifuged at 500xg for 10 min at 4 °C and supernatant (cytoplasm) was discarded. Nuclei were gently resuspended with transposition mix and incubated at 37 °C for 30 minutes at 1,000 rpm. DNA was purified using DNA Clean & Concentrator-5 (Zymo Research, D4013) according to the manufacturer’s instructions. PCR amplification (library generation) was performed according to the previous study (Brunton, Garner et al. 2020). Library was purified using AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions.
description
normal
disease
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
AI_3
title