|
| Status |
Public on Jun 12, 2017 |
| Title |
shSmyd5_HP1_mESC |
| Sample type |
SRA |
| |
|
| Source name |
shSmyd5_mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
cell line: R1 ES cell
protocol: shSmyd5
chip antibody: Anti-HP1 antibody (Millipore)
|
| Growth protocol |
shLuc and shSmyd5 ES cells were grown in ESC media (LIF and GSK3i) without feeders and in the presence of 1ug/mL puromycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ES cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against HP1
|
| Data processing |
Basecalls performed using GAPipeline or CASAVA
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: BEDGRAPH
|
| |
|
| Submission date |
Jan 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin L Kidder |
| E-mail(s) |
benjamin.kidder@wayne.edu
|
| Organization name |
Wayne State University
|
| Department |
Oncology
|
| Lab |
Laboratory of Epigenomics
|
| Street address |
4100 John R St
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE94033 |
SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation [ChIP-Seq] |
| GSE94086 |
SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation |
|
| Relations |
| BioSample |
SAMN06256244 |
| SRA |
SRX2514283 |
