GSM3902500: ATAC-seq Experiment 2 - control condition (2h); Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Pancreas
Cell type
EndoC-BH1
NA
NA
Attributes by original data submitter
Sample
source_name
EndoC-BH1 cells
cell line
EndoC-BH1
treatment
control
timepoint
2h
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC-seq assay was performed in 4 independent replicates for each time point (2 and 24 hours) as previously described in (Buenrostro, et al. 2013). Briefly, 50,000 cells were isolated from their nuclei by incubating the cells in 300 μl cold lysis buffer for 25 min on ice and resuspending them after 5 and 15 min using a syringe with a 29G needle. The pellet was next washed in 100 μl of lysis buffer and centrifuged for 15 min at 500 g at 4°C. The transposition reaction was carried out in a 25 μl reaction mix containing 2 μl of Tn5 transposase, 12.5 μl of TD buffer (Nextera DNA Library Prep Kit, 15028212, Illumina, San Diego, USA) and 10.5 μl DEPC-treated water. The transposition reaction mix was incubated at 37°C for 1 h following inactivation by incubating for 30 min at 40°C after addition of 5 μl of clean up buffer (900 mM NaCl, 300 mM EDTA), 2 μl of 5% SDS and 2 μl of Proteinase K. Isolation of the tagmented DNA was performed with 2x SPRI beads cleanup (Agencourt AMPure XP, Beckman Coulter) and was eluted in 20 μl DEPC treated water. Two sequential 9-cycle PCR were performed in order to enrich for small tagmented DNA fragments.