Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Sox9

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
Sox9
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
35167852
Reads aligned (%)
85.2
Duplicates removed (%)
23.9
Number of peaks
39065 (qval < 1E-05)

mm9

Number of total reads
35167852
Reads aligned (%)
85.1
Duplicates removed (%)
24.0
Number of peaks
38977 (qval < 1E-05)

Base call quality data from DBCLS SRA