Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Neuro-2a
Tissue
Brain
Cell Type
Neuroblast
Disease
Neuroblastoma

Attributes by original data submitter

Sample

sample_name
DRS012567
sample comment
Input DNA analysis of ChIP from N2A cells treated with siRNAs against Fus, Ewsr1 and Taf15.

Sequenced DNA Library

library_name
Genome-wide analysis of the role of FUS in RNA polymerase II transcription
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
N2A cells in a 15-cm dish were subjected to crosslinking in 1% formaldehyde for 10 min at RT, then quenched with 125 mM glycine for 5 min. Cells were washed, and the cell pellets were suspended in 1 ml lysis buffer. The lysates were sheared to yield fragments of 100-300 bp. Samples were centrifuged to remove insoluble material, and the supernatant containing DNA-protein complexes was collected. 8WG16 Ab (2 ?g) and 20 ?l of Dynabeads proteinG were added to the chromatin lysate, and were incubated on a rocking platform overnight at 4 ?C. Immune-complexes were washed extemsively. Immune-complexes were eluted with elution buffer . The samples were added with 10 ?l of 5 M NaCl and 5 ?l of 5 mg/ml proteinase K, and incubated at 65 ?C for 4 hrs to reverse the DNA-protein crosslinks. The final DNA fragments were purified with QIAquick PCR Purification Kit (Qiagen). ChIP-DNAs were gel-purified and transformed into libraries using the NEB DNA library preparation kit for Illumina (cat # E6000L) according to the manufacturer's instructions, and sequenced on Hiseq2000 DNA sequencing instrument at Otogenetics Corp. Total input DNA was also sequenced.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
11608071
Reads aligned (%)
96.2
Duplicates removed (%)
8.2
Number of peaks
112 (qval < 1E-05)

mm9

Number of total reads
11608071
Reads aligned (%)
96.1
Duplicates removed (%)
8.3
Number of peaks
89 (qval < 1E-05)

Base call quality data from DBCLS SRA