title: DI_3
organism: Homo sapiens
description: 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.
attributes.tag: ENA first public
attributes.value: 2024-08-28
attributes.tag: External Id
attributes.value: SAMEA114349366
attributes.tag: INSDC center name
attributes.value: Department of Biological Sciences, The University of Texas at Dallas
attributes.tag: INSDC last update
attributes.value: 2023-09-11T18:24:28Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-13339:DI_3
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: GM12878
attributes.tag: cell_type
attributes.value: B lymphoblastoid
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: human
attributes.tag: disease
attributes.value: normal
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: blood
attributes.tag: sample name
attributes.value: E-MTAB-13339:DI_3
attributes.tag: scientific_name
attributes.value: Homo sapiens