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Sample GSM2686166 Query DataSets for GSM2686166
Status Public on Jan 29, 2018
Title THMYCN_139423_input
Sample type SRA
 
Source name Th-MYCN mouse
Organism Mus musculus
Characteristics tissue: THMYCN tumor
input: NONE
treatment: None
strain: Th-MYCN
barcode: GGTTGGAC
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 tumors 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 SAMN07280955
SRA SRX2960257

Supplementary file Size Download File type/resource
GSM2686166_THMYCN_139423_input.wig.gz 63.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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