|
| Status |
Public on Sep 21, 2015 |
| Title |
PRDM9A_H3K4me3_Input |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell description: embryonic kidney
prdm9 allele: PRDM9A
ChIP: input
antibody manufacturer: NA
antibody catalog number: NA
antibody lot/batch#: NA
|
| Treatment protocol |
Cells were transfected using X-tremeGene HP transfection reagent (Roche) following manufacturer’s protocol using a ratio of 3:1 reagent to DNA with 10 µg total plasmid DNA.
|
| Growth protocol |
HEK293 cells were cultured in DMEM (Gibco, Life Technologies) supplemented with 10% FBS (Gibco) at 37 ºC and 5% CO2. 24 hours prior to transfection, cells were seeded at with 10 ml 2.5·105 cell/ml in 10 cm culture treated plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Kapa Hyper Prep Kits (Kapa Biosystems)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-Seq reads were aligned to the hg19 genome assembly using BWA v.0.5.10
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
Genome_build: hg19
|
| |
|
| Submission date |
Apr 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Lee Baker |
| E-mail(s) |
christopher.baker@jax.org
|
| Phone |
2072886365
|
| Organization name |
The Jackson Laboratory
|
| Department |
Research
|
| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE67673 |
Genome-wide map of H3K4me3 in HEK293 cells after PRDM9 expression |
|
| Relations |
| BioSample |
SAMN03465473 |
| SRA |
SRX985314 |
