Homo sapiens
Protocols: Cells were seeded on 10cm plates for 48 hours. To harvest, cells were washed once in PBS, incubated with cytoplasmic lysis buffer (50 mM HEPES pH7.9, 10 mM KCl2, 1.5 mM MgCl2, 0.34 M sucrose, 0.5% triton, 10% glycerol, 1 mM DTT and 0.1mg/mL RNase A) for 10 minutes at room temperature, washed once in cytoplasmic lysis buffer and finally scraped in genomic extraction buffer (50mM Tris pH 8.0, 5mM EDTA, 1% SDS, 0.5mg/mL proteinase K (Thermo, 25530049).  Lysates were transferred to 2mL DNA LoBind microcentrifuge tubes (Fisher Scientific, 0030108426) and incubated at 60 °C with 500rpm agitation for 1 hour. Sodium acetate pH 5.2 was added to a final concentration of 300mM and 2.5 volumes of 100% ethanol was added. Samples were incubated on ice for 1 hour to precipitate the genomic DNA and pelleted at 21,000g for 20 minutes at 4 °C. Genomic DNA pellets were washed once in 75% ethanol and re-pelleted for 10 minutes before being allowed to air-dry and be resuspended in nuclease free water.  DNA samples were diluted to 100ng/µL in 300µL in 1.5mL Bioruptor Plus TPX Microtubes (Diagenode, C30010010-300) and sonicated in a Bioruptor Plus sonicator for 20 cycles of 30 seconds on/30 seconds off with active chilling at 4 °C, shearing the DNA to an average length of ~600-800bp. 500ng of sheared genomic DNA was used for library preparation using the IDT xGen DNA library preparation kit (IDT, at 10009861) coupled to the xGen Exome Hyb Panel v2 for exome enrichment (IDT, 10005151) all according to the manufacturer instructions.
ENA first public
2024-12-09
INSDC center name
University of Cambridge
INSDC status
public
Submitter Id
E-MTAB-14219:HAP1
broker name
ArrayExpress
cell_line
HAP-1
cell_type
Chronic myeloid leukemia
collection date
not collected
common name
human
developmental stage
N/A
disease
myeloid leukemia
geographic location (country and/or sea)
not collected
individual
HAP1
isolate
not applicable
sample name
E-MTAB-14219:HAP1
scientific_name
Homo sapiens