|
| Status |
Public on Jan 29, 2018 |
| Title |
CG_input |
| Sample type |
SRA |
| |
|
| Source name |
Th-MYCN mouse
|
| Organism |
Mus musculus |
| Characteristics |
tissue: celiac ganglia
input: NONE
treatment: None
strain: Th-MYCN
barcode: GGCTACAG
chip antibody: NA
chip antibody vendor: NA
chip antibody cat. #: NA
|
| Growth protocol |
All experimental protocols were monitored and approved by The Institute of Cancer Research Animal Welfare and Ethical Review Body, in compliance with guidelines specified by the UK Home Office Animals (Scientific Procedures) Act 1986 and the United Kingdom National Cancer Research Institute guidelines for the welfare of animals in cancer research (Workman et al., 2010). Th-MYCN mice were genotyped to detect the presence of human MYCN transgene 27. Palpable intra-abdominal tumors or ganglia from Th-MYCN mice at 12-14 days of age were dissected and harvested for ChIP and immunohistochemistry.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP, tumors and ganglia were immediately flash frozen in liquid nitrogen and stored at -80°C. For immunohistochemistry, tumor and ganglia tissue were immediately fixed in 4% paraformaldehyde before being processed.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Chromatin whole cell extract input control in celiac ganglia from Th-MYCN mice
|
| Data processing |
Sequenced reads were aligned to MM9 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: mm9
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format
|
| |
|
| Submission date |
Jun 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE80154 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma |
| GSE100538 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [ChIP-seq Th-MYCN] |
|
| Relations |
| BioSample |
SAMN07280967 |
| SRA |
SRX2960245 |
