|
| Status |
Public on May 01, 2019 |
| Title |
Nf1fl/fl;DhhCre neurofibroma cells_Input DNA |
| Sample type |
SRA |
| |
|
| Source name |
Primary Nf1fl/fl;DhhCre mouse neurofibroma cells
|
| Organism |
Mus musculus |
| Characteristics |
stain: C57BL/6-I129
genotype/variation: Nf1fl/fl;DhhCre
cell type: primary neurofibroma cells
|
| Treatment protocol |
The Runx1 in-house Antibody was obtained from Yoram Groner (PLoS Genet. 2015 Aug 14;11(8):e1005457. doi: 10.1371/journal.pgen.1005457. eCollection 2015 Aug.)
|
| Growth protocol |
Primary Nf1fl/fl;DhhCre mouse neurofibroma cells were used for the Chromatin immunoprecipitation (CHIP) assay according to Magna CHIP TM instruction (Millipore, Billerica, MA)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Input DNA as control
run2116_lane1_read1_indexA011=mouse-IgG-JQ
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 v2.2.6
Peaks were called using HOMER v4.9
Genome_build: mm10
Supplementary_files_format_and_content: A peak calling file was generated and annotated using HOMER, TDF file were generated using IGV.
|
| |
|
| Submission date |
Nov 20, 2018 |
| Last update date |
May 02, 2019 |
| Contact name |
Kwangmin Choi |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Experimental Hematology & Cancer Biology
|
| Street address |
333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE122775 |
Runx1 and Runx3 cooperatively repress Pmp22 to drive neurofibromagenesis [ChIP-seq] |
| GSE122777 |
Runx1 and Runx3 cooperatively repress Pmp22 to drive neurofibromagenesis |
|
| Relations |
| BioSample |
SAMN10456712 |
| SRA |
SRX5036627 |
