Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
HGPS AG01972
patient id
AG01972
condition
HGPS
antibody
IgG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei pellets were resuspended in Covaris with 2mL of lysis buffer 3 (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% Na-Laurylsarcosine) and sheared using a Covaris S2 sonicator (20% duty cycle, intensity 5, 200 cycles/burst) for 9 minutes per sample. 300ug of chromatin was used for each sample. Before addition of antibodies, an aliquot of each sample was reserved for input control. After reverse cross-linking and cleanup, approximately 20ng of each sample was prepared for sequencing using the ChIP-seq sample rep kit (Illumina) according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
17576897
Reads aligned (%)
83.4
Duplicates removed (%)
69.6
Number of peaks
99 (qval < 1E-05)

hg19

Number of total reads
17576897
Reads aligned (%)
82.8
Duplicates removed (%)
71.0
Number of peaks
123 (qval < 1E-05)

Base call quality data from DBCLS SRA