|
| Status |
Public on May 19, 2011 |
| Title |
Lsh-/- H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Lsh-/- H3K4me3 sequence
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryonic fibroblast
antibody: anti-histone 3 lysine 4 trimethylation (anti-H3K4me3) (Abcam)
genotype/variation: Lsh-/-
|
| Treatment protocol |
Lshâ/â and WT mouse embryonic fibroblast (MEF) cell lines (20,000,000 cells) were treated with MNase to generate mostly mononucleosomes, and chromatin was precipitated with anti-histone 3 lysine 4 trimethylation (anti-H3K4me3) (Abcam).
|
| Growth protocol |
Lsh-/- and Lsh+/+ mouse embryonic fibroblasts (MEF) were grown in DMEM (Invitrogen/GIBCO) supplemented with 10% fetal bovine serum, 2 mM L-glutamine and antibiotics (Invitrogen/GIBCO).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA purified from precipitated chromatin from WT (Lsh+/+) or Lshâ/â MEFs with anti-H3K4me3 antibody. The ChIP DNA ends were repaired using PNK and Klenow enzymes (ER0720; Epicenter Biotechnology), followed by treatment with Taq polymerase I to generate a protruding 3â² A base used for adaptor ligation. Following ligation of a pair of Illumina adaptors to the repaired ends, the ChIP DNAs were amplified using the adaptor primers for 20 cycles and fragments of 200 to 400 bp were isolated from a 2% agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer 2Ã following manufacturer protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sequence tag
|
| Data processing |
The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer 2Ã following manufacturer protocols.
Sequenced tags were mapped to the mouse genome (Mm8) (tag number per 200-bp window) using the Illumina Analysis Pipeline
Peaks represent frequency of readout
|
| |
|
| Submission date |
May 19, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jigui Shan |
| E-mail(s) |
shanj@mail.nih.gov
|
| Organization name |
NCI-Frederick
|
| Street address |
430 Miller Dr
|
| City |
Frederick |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE29393 |
H3K4me3 modification analysis comparing Lsh WT and Lsh-/- MEFs |
| GSE29395 |
Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences |
|
| Relations |
| SRA |
SRX063911 |
| BioSample |
SAMN00619127 |
