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Sample GSM2700776 Query DataSets for GSM2700776
Status Public on Dec 22, 2017
Title SKNAS H3K27ac [Lab: Look]
Sample type SRA
 
Source name Neuroblastoma
Organism Homo sapiens
Characteristics cell type: SKNAS
chip antibody: H3K27ac
antibody vendor: Abcam
antibody catalog: ab4729
antibody lot: GR312651-1
young_id: 20170617_5868
Growth protocol Cells were cultured according to the suggested guidelines in RPMI media containing 10% FBS and 1% Penicillin-Streptomycin
Extracted molecule genomic DNA
Extraction protocol Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
 
Submission date Jul 12, 2017
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL18573
Series (2)
GSE101295 c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification (ChIP-Seq)
GSE101297 c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification
Relations
BioSample SAMN07346072
SRA SRX2997581

Supplementary file Size Download File type/resource
GSM2700776_20170617_5868.8186.rpm.WIG.gz 48.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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