Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Striatal progenitor cells
NA
NA

Attributes by original data submitter

Sample

source_name
Striatal Progenitor Cells
strain
C57BL/6
genotype
mutant (STHdhQ111/Q111)
treatment
serum starvation
chip-antibody
Normal rabbit IgG (Santa Cruz Biotechnology, sc-2027)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were washed once with 1X DPBS and then cross-linked. The cross-linked material was then rinsed, pelleted, and frozen in liquid nitrogen for later use. Frozen cell pellets were resuspended in lysis buffer and sonicated to shear DNA. Sheared DNA was immunopercipitated with anti-Histone H3 (acetyl K9) antibody. A negative control ChIP reaction was performed using normal rabbit IgG. The immunopercipitate was washed on protein G beads and reverse crosslinked with Proteinase K at 62 o C for 4 hours. Libraries were prepared with NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
22260277
Reads aligned (%)
81.6
Duplicates removed (%)
24.0
Number of peaks
368 (qval < 1E-05)

mm9

Number of total reads
22260277
Reads aligned (%)
81.5
Duplicates removed (%)
24.1
Number of peaks
388 (qval < 1E-05)

Base call quality data from DBCLS SRA