|
| Status |
Public on Jan 02, 2013 |
| Title |
48hr_H3K4me3_ChipSeq |
| Sample type |
SRA |
| |
|
| Source name |
Chromatin IP against 48hr_H3K4me3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: H1 embryonic stem cells
chip antibody: H3K4me3
antibody catalog number: Millipore 07-473
drug treatment: Activin
drug concentration: 50ng/ml
duration of treatment: 48hr
|
| Growth protocol |
H1 cells were grown to confluence in mTESR1 media. Cells were then differentiated for 48 hours in RPMI-B27 plus 50 ng/ml Activin
|
| 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. Sample was divided into 6 aliquots after sonication. 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 HiSeq 2000 |
| |
|
| Description |
02162012_C089EACXX_2.AGTCAA
|
| Data processing |
For all ChIP-Seq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 10 -n 2 -l 40 --best --strata.
supplementary_files_format_and_content: WIG files: For the ChIP-Seq samples, reads were extended 200 bp upstream and 0bp downstream (with respect to strand) and reads from both strands were allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 0.5 read per million are shown.
Images analysis and base calling was done using the solexa pipeline.
Genome_build: hg18
|
| |
|
| Submission date |
Sep 19, 2012 |
| 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 |
GPL11154 |
| Series (1) |
| GSE41009 |
Divergent transcription of lncRNA/mRNA gene pairs in embryonic stem cells |
|
| Relations |
| SRA |
SRX188843 |
| BioSample |
SAMN01179600 |
