|
| Status |
Public on May 28, 2012 |
| Title |
H3K4me1_stim_DC |
| Sample type |
SRA |
| |
|
| Source name |
H3K4me1_stim_DC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: dendritic cells
chip antibody: anti-H3K4me1 (clone CMA302)
|
| Treatment protocol |
stimulated for 2h with 100ng/ml LPS
|
| Growth protocol |
Bone marrow-derived progenitor cells were cultured in 20ng/ml each of SCF, IL-3 and IL-6, retrovirally infected using the pSir-delta U6CHisD vector carrying a hairpin directed against the JmjD2d coding sequence, and selected using 2mM histidinol. Dendritic cells were differentiated from progenitor cells in GM-CSF (4% X63-GMCSF supernatant) + 5ng/ml SCF for 4 days, followed by GM-CSF alone for 4 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using sonicated extracts from formaldehyde-fixed nuclei. Immunoprecipitated or input DNA was re-sonicated to obtain a mean fragment size of around 300bp, ligated to adapters using the NEBNext kit (New England Biolabs), and amplified by PCR (18 cycles). Sequencing was performed using single reads of 36bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
dendritic cells, 2h after stimulation with 100ng/ml LPS
|
| Data processing |
Sequence reads were aligned to the mm9 reference genome using the bowtie program, allowing for up to 2 mismatches.
Fragment midpoints were summed in 200bp windows to generate wig files.
Summits (of peaks) were identified using MACS 1.4 with paramaters p=1e-4, nomodel, nolambda, shift=150, to generate bed files.
|
| |
|
| Submission date |
Sep 26, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Dominic van Essen |
| Organization name |
Institute for Research on Cancer & Aging, Nice (IRCAN)
|
| Lab |
Transcription specificity
|
| Street address |
28 Avenue Valombrose
|
| City |
Nice |
| ZIP/Postal code |
06107 |
| Country |
France |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE32380 |
Identification of candidate enhancer elements in unstimulated and stimulated dendritic cells and fibroblasts |
| GSE32381 |
Cell-type specific control of enhancer activity by H3K9 trimethylation |
|
| Relations |
| SRA |
SRX099250 |
| BioSample |
SAMN00727979 |
| Named Annotation |
GSM801533_H3K4me1_stim_DC.wig.gz |
