|
| Status |
Public on Jan 03, 2012 |
| Title |
H3K4me1_TCP_48HR_ChipSeq |
| Sample type |
SRA |
| |
|
| Source name |
ZHBTc4 ES cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: H3K4me1
antibody catalog number: Abcam AB8895
antibody lot number: 961813
cell type: Embryonic stem cells
duration of treatment: 48 hr
drug: TCP
|
| Growth protocol |
ZHBTc4 Oct4 shutdown inducible cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media. Oct4 shutdown was induced by addition of 2ug doxycycline for 48 hours.
|
| 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 H3K4me1
|
| 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 |
SRX047147 |
| BioSample |
SAMN00217291 |
