|
| Status |
Public on Jan 03, 2012 |
| Title |
HDAC2 mES biological replicate |
| Sample type |
SRA |
| |
|
| Source name |
Embyonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: HDAC2
antibody catalog number: Abcam AB7029
antibody lot number: 769177
cell type: V6.5 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 two passages 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 150 and 300bp (representing shear fragments between 50 and 200nt 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 HDAC2
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
See Supplemental Information of associated manuscript for details regarding generation of WIGs.
|
| |
|
| Submission date |
Mar 08, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE27841 |
Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation (ChIP-seq) |
| GSE27844 |
Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation |
|
| Relations |
| SRA |
SRX047139 |
| BioSample |
SAMN00217283 |
