Illumina HiSeq 4000 paired end sequencing; ATAC-seq in Renal Cell Carcinoma cell lines
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Kidney
Cell type
Caki-1
Primary Tissue
Kidney
Tissue Diagnosis
Adenocarcinoma Clear Cell
Attributes by original data submitter
Sample
ENA first public
2019-06-28
ENA last update
2019-04-03
ENA-CHECKLIST
ERC000011
External Id
SAMEA5547875
INSDC center alias
Novartis Institutes for Biomedical Research
INSDC center name
Novartis Institutes for Biomedical Research
INSDC first public
2019-06-28T04:03:11Z
INSDC last update
2019-04-03T12:06:59Z
INSDC status
public
Submitter Id
E-MTAB-7844:caki1_1
broker name
ArrayExpress
cell line
Caki1
cell type
epithelial cell
common name
human
disease
clear cell renal carcinoma
genotype
doxycycline inducible PAX8 knockdown
organism part
kidney
sample name
E-MTAB-7844:caki1_1
Sequenced DNA Library
library_name
caki1_1_p
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
PCR
library_construction_protocol
150000 Cells were lysed in ATAC-lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately processed for tagmentation. Tagmentation was performed as described in Buenrostro et al. Curr Protoc. Mol. Biol., 2016 using the Illumina Nextera Tn5 Transposase. ATAC-seq libraries were amplified from the tagmentation reaction by PCR using the PPC (PCR Primer mix) from the Illumina Nextera Tn5 Transposase kit and adding barcodes from the Nextera Index Kit (24 indexes 96 samples). DNA was purified using AmpPure XP beads.