Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Liver
Cell type
AML12
Tissue
Liver
Cell Type
Hepatocyte
Disease
Normal

Attributes by original data submitter

Sample

source_name
Input
cell line
AML12
genotype/variation
BirA HNRNPU
chip antibody
Input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
BirA-ChIP seq experiments were performed as described (PMID: 22412018). Briefly, 1*10^7 cells were fixed with 4% formaldehyde for 10min at RT, and then the cells were divided into six part equally. Cells were lysed at 25°C in 200ul lysis buffer for 5 min.After cell lysis, the chromatin was sonicated by the Bioruptor sonicator. The cell lysate was centrifuged at 17,000g for 15min at 4°C. Supernatants were incubated with 30 μl High Capacity Streptavidin Agarose (Thermo Fisher Scientific) overnight. Beads were washed twice for 5 min with buffer 1 (2% SDS) at 25°C,once with buffer 2,once with buffer 3 and twice with buffer 4. Lastly, adding 60μl Elution buffer to the beads, and then placed in a 70°C water bath overnight with shaking. ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina MiSeq

mm10

Number of total reads
50107624
Reads aligned (%)
96.4
Duplicates removed (%)
19.1
Number of peaks
341 (qval < 1E-05)

mm9

Number of total reads
50107624
Reads aligned (%)
96.1
Duplicates removed (%)
19.0
Number of peaks
428 (qval < 1E-05)

Base call quality data from DBCLS SRA