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| Status |
Public on Jun 30, 2011 |
| Title |
H3K9me3_ChIPSeq |
| Sample type |
SRA |
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| Source name |
Pancreatic islets_H3K9me3
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| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
age: 8-10 week old
tissue/cell type: hand-picked pancreatic islets
chip antibody: H3K9me3 (Abcam ab8898 lot AP248039)
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| Growth protocol |
Islets were purified by collagenase digestion, filtration through a 70um filter with subsequent hand picking, livers were perfused and homogenized.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% formaldehyde and incubated at room temperature (RT) for 10min, prior to the addition of glycine to 0.125M followed by incubation at RT for 5min. Cells were pelleted, washed and resuspended in 500ul ChIP cell lysis buffer (10mM Tris-Cl, pH 8.0, 10mM NaCl, 3mM MgCl2, 0.5% NP-40) containing 1x protease inhibitor cocktail (Thermo Scientific, Waltham, MA, USA). Cells were then rehomogenized, incubated on ice for 5min and repelleted. The pellet was resuspended in 400ul ChIP nuclear lysis buffer (1% SDS, 5mM EDTA, 50mM Tris-Cl, pH 8.1) supplemented with protease inhibitor cocktail tablets (Thermo Scientific). Cells were sonicated in ice-water bath (Sonicator 3000, Misonix, Farmingdale, NY, USA) for 24 cycles of 30s on, 30s off. Samples were pelleted to remove cellular debris and transferred to fresh tubes.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Chromatin IP against H3K9me3
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| Data processing |
Alignment: Sequence reads were mapped to mm9 (NCBI 37) using BWA (v 0.5.7) and default parameters.
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| Submission date |
Jun 29, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Plettner |
| E-mail(s) |
pplettner@bcgsc.ca
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| Organization name |
BC Cancer Agency GSC
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| Street address |
100-570 West 7th Avenue
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| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 4S6 |
| Country |
Canada |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE30298 |
Identification and analysis of pancreatic islet specific enhancers |
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| Relations |
| SRA |
SRX081535 |
| BioSample |
SAMN00631863 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM751033_301MYAAXX_6_export.txt.gz |
352.5 Mb |
(ftp)(http) |
TXT |
| GSM751033_30WK2AAXX_3_export.txt.gz |
465.4 Mb |
(ftp)(http) |
TXT |
| GSM751033_30WK2AAXX_4_export.txt.gz |
443.2 Mb |
(ftp)(http) |
TXT |
| GSM751033_30WK2AAXX_5_export.txt.gz |
433.9 Mb |
(ftp)(http) |
TXT |
| GSM751033_H3K9me3_MM0408_4L_mm9_xset200_dupsN_ht3.wig.gz |
50.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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