|
| Status |
Public on Feb 13, 2013 |
| Title |
ChipSeq for H3K4 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: H3K4me3
antibody vendor and catalog number: Abcam AB8580
background strain: C57BL/6-129
|
| 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 |
| |
|
| Description |
Chromatin IP against H3K4 (10^7)
cell number: 10 million
|
| 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 with parameters -e 70 -k 1 -m 1 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended by MACS and allocated into 50bp bins
|
| |
|
| Submission date |
Feb 12, 2013 |
| 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 |
GPL9185 |
| Series (2) |
| GSE44286 |
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes [ChIP-Seq] |
| GSE44288 |
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes |
|
| Relations |
| SRA |
SRX236480 |
| BioSample |
SAMN01920468 |
