Illumina HiSeq 2000 sequencing; ATAC-seq for L3.6pl cells
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Pancreas
Cell type
L3.6
NA
NA
Attributes by original data submitter
Sample
ENA first public
2018-12-18
ENA last update
2018-07-20
ENA-CHECKLIST
ERC000011
External Id
SAMEA4799826
INSDC center alias
Section of Tumor Epigenetics, Department of General, Visceral and Pediatric Surgery, University Medical Center Gottingen, 37075 Gottingen, Germany
INSDC center name
Section of Tumor Epigenetics, Department of General, Visceral and Pediatric Surgery, University Medical Center Gottingen, 37075 Gottingen, Germany
INSDC first public
2018-12-18T17:02:52Z
INSDC last update
2018-07-20T14:53:24Z
INSDC status
public
Submitter Id
E-MTAB-7035:L3.6pl_ATAC_C2
broker name
ArrayExpress
cell line
L3.6pl
cell type
epithelial cell
common name
human
disease
pancreatic adenosquamous carcinoma
metastatic site
celiac lymph node
organism part
pancreas
sample name
E-MTAB-7035:L3.6pl_ATAC_C2
Sequenced DNA Library
library_name
L3.6pl_ATAC_C2_s
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC was performed following the protocol of Buenrostro et al. Briefly, 50,000 L3.6pl cells were trypsinized and washed twice with cold PBS. Then cells were re-suspended in lysis buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and incubated for 15 minutes at a rotating wheel at 4ºC followed by centrifugation and in re-suspended in 50 µl of transposition mix composed of 2.5µl of TDE1 (Nextera Tn5 Transposase), 25 µl TD (2x reaction buffer) in nuclease free water (Nextera DNA Library Prep Kit, FC-121-1030, Illumina). Then it was incubated at 37 degrees for 30 minutes. MinElute PCR Purification kit (Qiagen) was used for DNA extraction following the instructions of the manufacturer. ATAC libraries were made using the Nextera DNA Library Prep Kit according to Buenrostro et al. The libraries were amplified for 15 cycles in total of: 98ºC for 10 seconds, 63ºC for 30 seconds, and 72ºC for 60 seconds.