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Status |
Public on May 01, 2019 |
Title |
Nf1fl/fl;DhhCre neurofibroma cells_Input DNA |
Sample type |
SRA |
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|
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.)
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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)
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|
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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.
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|
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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 |