Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Epitope tags

Cell type

Cell type Class
Neural
Cell type
Hippocampal neurons
NA
NA

Attributes by original data submitter

Sample

source_name
Primary hippocampal neurons
strain
C57BL/6J
cell type
hippocampal neuron
passages
DIV11
treatment
transduced with AAV8-hSyn-Satb2-V5 at DIV4
antibody
anti-V5 tag antibody (Abcam, catalog# 15828)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Hippocampal neurons were cross-linked with formaldehyde at 1% final concentration for 10 min at room temperature, and chromatin was prepared using the Zymo-Spin ChIP kit (Zymo Research) following manufacturer's instructions. Sonication was performed at high power setting for 40 cycles (30 s ON, 30 s OFF) using a Bioruptor Plus (Diagenode Inc., Denville, NJ), yielding fragment size range of 200-700 bp. ChIP assays were performed in triplicates using 20 μg of chromatin and 10 μg of anti-V5 tag antibody (ab15828). IgG (12-370, Millipore) was included as a negative control. ChIP DNA was purified using ChIP DNA Clean and Concentrator (Zymo Research) and the relative abundance of a control region in V5-immunoprecipitated DNA was quantified by qPCR with sequence-specific primers. DNA libraries (Satb2-ChIP and Input control DNA) were prepared and sequenced on a HiSeq 2000 sequencer (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
11632563
Reads aligned (%)
90.7
Duplicates removed (%)
48.3
Number of peaks
467 (qval < 1E-05)

mm9

Number of total reads
11632563
Reads aligned (%)
89.9
Duplicates removed (%)
48.4
Number of peaks
520 (qval < 1E-05)

Base call quality data from DBCLS SRA