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Status |
Public on Jul 01, 2015 |
Title |
Nasal_Chondrocyte_Input_Control_ChIPseq |
Sample type |
SRA |
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Source name |
E17.5 Nsal chondrocytes
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Organism |
Mus musculus |
Characteristics |
strain background: ICR isolation stage: E17.5 cell type: Enzyme digested nasal septum chondrocytes
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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 |
SAMN03703606 |
SRA |
SRX1035120 |
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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