Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Bone
Cell type
Chondrocytes
MeSH Description
Polymorphic cells that form cartilage.

Attributes by original data submitter

Sample

source_name
p1 mouse rib chondrocytes
strain background
ICR
isolation stage
p1
cell type
Enzyme digested rib chondrocytes
chip antibody
H3K27Me3
chip antibody vandor
Millipore

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryonic day 17.5 (E17.5) nasal septum or postnatal day 1 (p1) rib chondrocytes isolated from wild-type ICR mice were immediately cross-linked with 1% formaldehyde for 10 minutes at room temperature, then 0.125 M Glycine was added to quench formaldehyde. 20,000,000 cells were used for a ChIP reaction. Chromatin was sonicated by 10 sessions of 30 pulses (1 sec on and 1 sec off) at 50% amplitude using the Branson sonifier 250D (Branson Ultrasonics Corporation, Danbury, CT) in order to obtain 100 – 600 bp of DNA fragments. One hundred microlitters of Dynabeads M-280 Sheep anti-Mouse IgG or anti-Rabbit IgG was combined with 9 μg of antibodies for targets of interest. ChIPseq libraries were constructed from input control samples (input DNA and IgG controls) as well as ChIP DNA using ChIP-seq DNA Sample Prep Kit (IP-102-1001; Illumina Inc., San Diego, CA), according to manufacturer’s instruction. Adaptor-modified DNA fragments were enriched by 18 cycles of PCR.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

mm10

Number of total reads
28089701
Reads aligned (%)
90.1
Duplicates removed (%)
11.0
Number of peaks
1173 (qval < 1E-05)

mm9

Number of total reads
28089701
Reads aligned (%)
90.0
Duplicates removed (%)
11.1
Number of peaks
1182 (qval < 1E-05)

Base call quality data from DBCLS SRA