|
| Status |
Public on Oct 31, 2010 |
| Title |
ChIP-Seq for H3K4me3 in ES (129JAE-C57/B6) cells |
| Sample type |
SRA |
| |
|
| Source name |
Embyonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: H3K4me3
antibody catalog number: Abcam AB8580
cell type: embryonic stem cells
|
| Growth protocol |
V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 200 and 350bp (representing shear fragments between 100 and 250nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against H3K4me3
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using MAQ (phred score 50).
For all samples aligned sequences were extended 600bp upstream and 400bp downstream (with respect to read strand) for transcription histone marks and and 200bp upstream and 0bp downstream (with respect to read strand) for transcription factors, allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
|
| |
|
| Submission date |
Sep 16, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Menno P Creyghton |
| E-mail(s) |
m.creyghton@hubrecht.eu
|
| Organization name |
Hubrecht Institute
|
| Lab |
Creyghton
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE24164 |
ChIP-Seq of chromatin marks at distal enhancers in Mouse Embryonic Stem Cells and adult tissues. |
| GSE24165 |
Histone H3K27ac separates active from poised enhancers and predicts developmental state |
|
| Relations |
| SRA |
SRX027334 |
| BioSample |
SAMN00113685 |
| Named Annotation |
GSM594581_MC5_ES_H3K4me3_wig_min0.5.WIG.gz |
