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| Status |
Public on Dec 08, 2018 |
| Title |
H3K4me2_WT_ChIPSeq |
| Sample type |
SRA |
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| Source name |
WT_BM-derived MSPCs
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Wild type
cell type: BM-derived Mesenchymal stem/progenitor cells (MSPCs)
cell type: BM-derived MSPCs
passages: 5-10
chip antibody: H3K4me2 (Active Motif 39141)
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| Growth protocol |
Bone marrow–derived mesenchymal stem/progenitor cells were cultured with MSC medium (MesenCult basal media plus 20% of MesenCult Supplemental), and replated when the cultures reached 80-90% confluency.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
MSPCs were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 300 to 500 bp. Histone-DNA complexes were isolated with specific histone modification antibodies.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Basecalls performed using Illumina NextSeq 500
ChIP-Seq reads were aligned to the mm10 genome assembly using the BWA algorithm with default settings
Data were filtered using the following specifications:only reads that pass Illumina's purity filter,aligned with no more than 2 mismatches,and map uniquely to the genome were used in the subsequent analysis,than duplicate reads were removed.
peaks were called using SICER version 1.1 with the following setting:Threshold for redundancy allowed for ChIP reads(1),window size(200bp) ,FDR cutoff(1E-10)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file format,it contains peaks position imformation such as chromosome,peaks start and end positions.
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| Submission date |
Dec 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Caiying Zhu |
| E-mail(s) |
[email protected]
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| Phone |
13622053408
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| Organization name |
Institute of Hematology & Blood Diseases Hospital
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| Street address |
NO. 288 Nanjing Road, Heping District, Tianjin
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| City |
Tianjin |
| ZIP/Postal code |
300020 |
| Country |
China |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE75786 |
Loss of Asxl1 Alters Mesenchymal Stem Cell Fate through H3K4me3 [ChIP-seq] |
| GSE75788 |
Loss of Asxl1 Alters Mesenchymal Stem Cell Fate through H3K4me3 |
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| Relations |
| SRA |
SRX1471727 |
| BioSample |
SAMN04326718 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1968335_H3K4me2_WT.peaks.txt.gz |
343.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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