Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ORC1

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Hela cell
cell line
Hela cell
transfection
siH2A.Z
genotype/variation
H2A.Z-KO
antibody
ORC1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For native ChIP-seq, cells were collected and digested by MNase to get the mono-nucleosome. For BrdU-IP-seq, genomic ChIP-seq: DNA were extracted from cells and then sonicated to 200-500bp. Libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq. NS-seq: The genomic DNA was extracted by DNAzol. Then the DNA was denatured by boiling 10 mins at 100 °C and loaded onto 30ml neutral 5%-30% sucrose gradients. The mixture was centrifuged in SW28 rotor at 25000rpm for 20 hours. 1 ml-fraction was withdrawn from the top of the gradients. DNA fragments ranged from 0.5-2.5Kb were collected and purified. Half of the total purified DNA was treated with RNAase A. NS-seq: The single strand DNA was converted to double strand DNA by BioPrime Array CGH Genomic Labeling System (life technology). DNA library for Immunila was prepared using a NEBNext Ultra DNA Library Prep Kit (NEB) according to the manufactory's instruction. RNA-seq: RNA was extracted using Trizol (Invitrogen) according to the manufacturer's instruction. RNA-seq: For RNA-seq, libraries were prepared according to the Illumina TruSeq protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
21389952
Reads aligned (%)
93.3
Duplicates removed (%)
5.0
Number of peaks
631 (qval < 1E-05)

hg38

Number of total reads
21389952
Reads aligned (%)
94.6
Duplicates removed (%)
4.2
Number of peaks
509 (qval < 1E-05)

Base call quality data from DBCLS SRA