GSM1607174: T131 Dnase1; Homo sapiens; DNase-Hypersensitivity
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
DNase-seq
Antigen
DNase-Seq
Cell type
Cell type Class
Unclassified
Cell type
Unclassified
NA
NA
Attributes by original data submitter
Sample
source_name
formalin-fixed paraffin-embedded tissue
patient
papillary thyroid carcinoma
cell type
tumor
Sequenced DNA Library
library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
For DNase I digestion, 0.2 to 1 unit of Dnase I was added to the cells and incubated at 37°C for 5 minutes. The reaction was stopped by adding 80 ul of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EDTA), 1 ul of 20mg/ml Proteinase K and 5 ul of 6ng/ul circular carrier DNA. The mixture was incubated at 55°C for 1 hour and DNA purified by Phenol-chloroform extraction, followed by precipitation with ethanol in the presence of glycogen. The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10"; 67°C, 30"; 72°C, 30" for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10"; 68°C, 30"; 72°C, 30" for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq2000.