Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
DICER1

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK 293 cells
cell line
HEK 293
dicer status
wt
chip antibody
Dicer

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 10 ng of the DNA sample was used for Illumina/Solexa sequencing in the following steps: 1) DNA samples were blunt-ended with T4 DNA polymerase and Klenow polymerase; 2) a dA base was added to the 3' end of each strand by Klenow (exo minus) polymerase; 3) Illumina's genomic adapters were ligated to the DNA fragments; 4) PCR amplification was performed to enrich ligated fragments; 5) Enriched product of ~300-400bp was cut out from gel and purified with QIAquick Gel Extraction Kit. The completed libraries were quantified by Agilent 2100 Bioanalyzer. The libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cell, amplified in situ. The libraries were then sequenced on the Genome Analyzer IIx following the SBS Sequencing 36 Cycle Kit v5 protocol.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
27767440
Reads aligned (%)
4.0
Duplicates removed (%)
33.2
Number of peaks
121 (qval < 1E-05)

hg38

Number of total reads
27767440
Reads aligned (%)
4.0
Duplicates removed (%)
32.7
Number of peaks
114 (qval < 1E-05)

Base call quality data from DBCLS SRA