|
| Status |
Public on Nov 18, 2013 |
| Title |
Runx3_NK_CHIP_Runx3_IP |
| Sample type |
SRA |
| |
|
| Source name |
Splenic NK cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Splenic NK cells
passages: Cells were freshly isolated, fixed and frozen at -80°C.
strain: ICR
chip antibody: Runx3 poly clonal home made
|
| Growth protocol |
ChIP-Seq experiments for detection of Runx3-bound genomic regions and H3K4me1-marked regions were conducted using in-house anti Runx3 Ab and monoclonal anti-H3K4me1 Ab, rspectively, with 40 million freshly isolated (resting) splenic NK cells isolated by negative selection using NK cell isolation kit (R&D) and sorting for NKp46+ cells. Isolated NK cells were fixed and frozen at -80°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 48ul of anti-Runx3 Ab, anti-H3K4me1 or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN).
For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina genome analyzer IIx according to the manufactures instructions by loading 15 pmoles of denatured library template onto separate lanes of a flow cell. Sequencing short reads (40 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
first IP experiment of Runx3
|
| Data processing |
CASAVA 1.7
For data analysis 25-30 million Runx3, H3K4me1 and NIS IP short read (40 bp) sequences were aligned uniquely to the mouse genome (mm9) using ELAND. Peaks of enriched Runx3 or H3K4me1 regions were detected using the uniquely aligned sequences (sorted file) of merged biological replicates of IP versus the NIS, using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4 done by scaling to small
|
| |
|
| Submission date |
Aug 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph Lotem |
| E-mail(s) |
joseph.lotem@weizmann.ac.il
|
| Phone |
972-8-934-2342
|
| Organization name |
Weizmann institute of science
|
| Department |
Molecular genetics
|
| Street address |
P.O.B 26
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE50127 |
Genome-wide maps of Runx3 bound regions in splenic NK cells |
| GSE50131 |
The transcription program of Runx3 in natural killer cells and CD8+ T cells |
|
| Relations |
| BioSample |
SAMN02324611 |
| SRA |
SRX338021 |
