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| Status |
Public on Jul 01, 2015 |
| Title |
Rib_Chondrocyte_H3K27me3_ChIPSeq |
| Sample type |
SRA |
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| Source name |
p1 mouse rib chondrocytes
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| Organism |
Mus musculus |
| Characteristics |
strain background: ICR
isolation stage: p1
cell type: Enzyme digested rib chondrocytes
chip antibody: H3K27Me3
chip antibody vandor: Millipore
chip antibody cat. #: 07-449
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| Treatment protocol |
Wild type, not treated
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| Growth protocol |
Neonatal ICR wild-type mice embryonic day 17.5 nasal septum or postnatal day 1 rib
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| Extracted molecule |
genomic DNA |
| Extraction 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
ChIP libraries were sequenced on Illumina Genome Analyzer II for samples (Rib_Chondrocyte_Sox9_ChIPseq, Rib_Chondrocyte_H3K4me2_ChIPSeq, Rib_Chondrocyte_H3K4me3_ChIPSeq, Rib_Chondrocyte_H3K27me3_ChIPSeq, Rib_Chondrocyte_H3K36me3_ChIPSeq, Rib_Chondrocyte_H3K27ac_ChIPSeq, Rib_Chondrocyte_RNA_Pol_II_ChIPseq, Rib_Chondrocyte_Input_Control_ChIpseq, Rib_Chondrocyte_IgG_Control_ChIpseq), or Hiseq 2000 for samples ( Rib_Chondrocyte_Input_Control_for_p300_ChIPseq, Rib_Chondrocyte_p300_ChIPSeq)
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 or an IgG control. Peaks were incorporated into further analysis displaying an FDR<0.01.
Genome_build: mouse mm9
Supplementary_files_format_and_content: bed
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| Submission date |
May 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinjun He |
| E-mail(s) |
xinjun.he@med.usc.edu
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| Phone |
323-442-8077
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| Organization name |
University of Southern California
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| Department |
BROAD CIRM Center
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| Street address |
1425 San Pablo St
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (2) |
| GSE69109 |
Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte [ChIP-seq] |
| GSE69111 |
Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte |
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| Relations |
| BioSample |
SAMN03703597 |
| SRA |
SRX1035111 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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