|
| Status |
Public on Nov 07, 2017 |
| Title |
H3K9me3_IL1RN |
| Sample type |
SRA |
| |
|
| Source name |
Ishikawa SID4x-dCas9-KRAB
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: H3K9me3
grna treatment: Enhancer-I
drug treatment: none
growth conditions: charcoal-stripped RPMI
|
| Growth protocol |
Cells were maintained in RPMI
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20 million cells per ChIP were crosslinked in 1% formaldehyde for 10 minutes at room temperature. Crosslinking was stopped with 125 mM Glycine and nuclei were extracted. Chromatin was sonicated using an Epishear Probe Sonicator (Active Motif) for 3 minutes at 40% power. c-MYC (D3N8F) antibody (Cell Signaling Technology) was used for immunoprecipitation and an input sample for each cell line served as the control.
Libraries were constructed using a standard Illumina library construction protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads in fastq format were aligned to hg19 using bowtie with the following parameters: -m 1 -t --best -q -S -l 32 -e 80 -n 2
Sam alignments were converted to sorted bams using samtools
Peaks were called with MACS2 using a p-value cutoff of 1e-10 and the mfold parameter bounded between 15 and 100
During peak calling, read pileups were stored as bedGraphs
Genome_build: Hg19
Supplementary_files_format_and_content: bigWigs contain read pileups generated from MACS2 bedGraphs
|
| |
|
| Submission date |
Jun 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jay Gertz |
| E-mail(s) |
jay.gertz@hci.utah.edu
|
| Organization name |
University of Utah
|
| Street address |
2000 Circle of Hope Dr.
|
| City |
Salt Lake City |
| ZIP/Postal code |
84103 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE99905 |
Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers [ChIP-Seq] |
| GSE99906 |
Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers |
|
| Relations |
| BioSample |
SAMN07212611 |
| SRA |
SRX2901945 |
