|
| Status |
Public on Feb 29, 2016 |
| Title |
Rib_Chondrocyte_Jun_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
p1 mouse rib chondrocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: chondrocytes
tissue: rib
developmental stage: p1
strain: ICR mice
chip antibody: Jun(Abcam Cat#ab31419)
|
| Treatment protocol |
Wild type, not treated
|
| Growth protocol |
Neonatal ICR wild-type mice postnatal day 1 rib cartilage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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-Rabbit IgG was combined with 9 μg of antibodies for Jun.
ChIPseq libraries were constructed with input control samples (input 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Enzyme digested rib chondrocytes
|
| Data processing |
ChIP libraries were sequenced on Illumina Hiseq 2000
the first 25nt of sequence reads were aligned with Eland software (Illumina), allowing not more than 2 mismatches per reads to mouse genome version mm9/Build 37
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008; Jiang et al., 2010) with a P-value cutoff of 10e-5, by comparing with the input control without antibody immunoprecipitation. Peaks were incorporated into further analysis displaying an FDR<0.01.
Genome_build: mouse mm9
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Sep 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinjun He |
| E-mail(s) |
xinjun.he@med.usc.edu
|
| Phone |
323-442-8077
|
| Organization name |
University of Southern California
|
| Department |
BROAD CIRM Center
|
| Street address |
1425 San Pablo St
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE73372 |
AP-1 family members act at DNA targets in conjunction with Sox9 to promote chondrocyte hypertrophy |
|
| Relations |
| BioSample |
SAMN04108629 |
| SRA |
SRX1281904 |
