|
| Status |
Public on May 28, 2012 |
| Title |
input_unstim_DC |
| Sample type |
SRA |
| |
|
| Source name |
input_unstim_DC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: dendritic cells
chip antibody: none
|
| Treatment protocol |
unstimulated
|
| 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 paired-end reads of 36bp each. Average insert size was around 270bp (sd 100bp) based on the mapped distances between read-pairs.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
dendritic cells, unstimulated
|
| 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 overlapping 2kb windows; the number of tags in ChIP samples was divided by the number of tags in the same window in the corresponding input sample (when this was greater than zero) to generate wig 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 (3) |
| GSE32377 |
Analysis of H3K9 trimethylation in unstimulated and stimulated dendritic cells and fibroblasts |
| 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 |
SRX099238 |
| BioSample |
SAMN00727969 |
