|
| Status |
Public on Oct 01, 2010 |
| Title |
H3K27me3 ChIPseq in human ES cells |
| Sample type |
SRA |
| |
|
| Source name |
Embyonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K27me3
antibody catalog number: Abcam AB6002
cell type: BGO3 (feeder free)
|
| Growth protocol |
hES cells were grown in mTESR media (Stem Cell Technologies) on plates coated with matrigel (BD Biosciences) in the absence of feeder cells.
|
| 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 H3K27me3 in human ES cells
|
| 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.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and 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 30, 2010 |
| 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 |
GPL9115 |
| Series (1) |
| GSE24463 |
H3K27me3, H3K79me2, and Suz12 ChIP-Seq in Human Embryonic Stem Cells (BG03). |
|
| Relations |
| SRA |
SRX027456 |
| BioSample |
SAMN00113776 |
| Named Annotation |
GSM602672_11182009_42YK9AAXX_B1.wig.gz |
