|
| Status |
Public on Jan 24, 2013 |
| Title |
Tot2, MSCV, Day3, anti-H3K4me1 |
| Sample type |
SRA |
| |
|
| Source name |
Tot2 cells, MSCV transuced, Day3
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Myeloid progenitor cell line Tot2 (derived from Irf8 knockout mouse)
culture condition: MSCV transduced
treatment period: 3 days
chip antibody: rabbit anti-H3K4me1 antibody (Ab8895, Abcam)
|
| Treatment protocol |
Retroviral preparation and transduction with control MSCV or MSCV-IRF8 were performed as described previously (Tamura et al. Blood 106: 1938, 2005). Cells were transduced by spinoculation in a retroviral supernatant supplemented with cytokines and 4 μg/ml polybrene. At 3 days after the transduction, the cells were harvested for chromatin immunoprecipitation.
|
| Growth protocol |
Myeloid progenitor cell line Tot2 cells derived from Irf8 knockout mouse were cultured in RPMI1640 supplemented with 2 mM L-Glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 20% fetal bovine serum and 5.0 ng/ml granulocyte-macrophage colony stimulating factor.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The lysates were sonicated and immunoprecipitation was then performed using anti-IRF8 antibody or anti-H3K4me1 antibody, coupled with magnetic Dynabeads-Protein A. Purified ChIP DNA was modified for end repair, adapter ligation and then separated by agarose gel electrophoresis to select DNA fragments between 170 and 230 bp. Gel-purifed DNA was amplified by PCR for ChIP-Seq library preparation according to the Illumina’s manuals. After verifying the qualities by Bioanalyzer (Agilent), eight pmol of each ChIP-Seq library was used directly for cluster generation on Cluster Station (Illumina). The sequencing analysis by Genome Analyzer IIx (Illumina) was performed according to the manufacturer’s manuals.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.７
Tag sequences were mapped on mouse genome sequences (mm9) by the Bowtie software with optional parameters “-a --best --strata -m 1 -v 2 -S mm9”.
Peaks were identified using the FindPeaks tool in the HOMER package with input DNA tags as background distribution, or identified using SICER (optional parameters “mm9 1 200 200 0.74 200 .01”) with input DNA tags as background distribution.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files reporting ChIP-Seq peaks with input DNA tags as background distribution
|
| |
|
| Submission date |
Jun 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tomohiko Tamura |
| E-mail(s) |
tamurat@yokohama-cu.ac.jp
|
| Organization name |
Yokohama City University
|
| Department |
Department of Immunology
|
| Street address |
3-9 Fukuura, Kanazawa-ku
|
| City |
Yokohama |
| ZIP/Postal code |
236-0004 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE38824 |
Analysis of TF binding sites and histone modification in IRF8-induced monocyte differentiation |
| GSE38825 |
IRF8-induced monocyte differentiation |
|
| Relations |
| SRA |
SRX155380 |
| BioSample |
SAMN01056993 |
