Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Brain
MeSH Description
The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.

Attributes by original data submitter

Sample

source_name
Brain cells
cell line
J1
cell type
Brain cells
differentiation days
differentiated
chip antibody
IgG (Santa Cruz, SC-2027)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cross-linked neuronal progenitor cells (2 days) and E15.5 mouse embryonic brain tissue were lysated, and neuclei were isolated. The nuclear pellet was re-suspended in 1 ml of cold shearing buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA, and 0.1% SDS) and chromatin was then sheared to 100-300 bp fragments using a Covaris S220 sonicator (Covaris; Woburn, MA) with the following settings; 12.5 min, 5% duty cycle, 140 Watts peak incident power, 200 cycles per burst. After adding 1% Triton X-100 and 150 mM NaCl (final concentrations) to the sheared chromatin and mixing, the solution was cleared by centrifugation at 14,000xg for 10 min at 4°C. Chromatin fragments were incubated with 2.5 μg of affinity purified anti-Tet3FL antibody (raised against a region of Tet3FL, amino acids 1-102) or IgG control (Santa Cruz; SC-2027) overnight at 4°C with rotation, and then immunoprecipitated using protein A magnetic beads (Millipore; Billerica, MA). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
39202940
Reads aligned (%)
92.9
Duplicates removed (%)
22.3
Number of peaks
278 (qval < 1E-05)

mm9

Number of total reads
39202940
Reads aligned (%)
92.8
Duplicates removed (%)
22.4
Number of peaks
220 (qval < 1E-05)

Base call quality data from DBCLS SRA