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Sample GSM2486159 Query DataSets for GSM2486159
Status Public on May 22, 2018
Title BE2C ISL1 [Lab: Look]
Sample type SRA
Source name Neuroblastoma
Organism Homo sapiens
Characteristics cell type: BE2C
chip antibody: ISL1
antibody manu.: DSHB
antibody catalog: 40.3A4
antibody lot: 8/22/13
young_id: 20161217_5288
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
Peaks were called using MACS 1.4 with parameters -p 1e-9 --keep-dup=auto and corresponding input control.
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 Feb 13, 2017
Last update date May 15, 2019
Contact name Richard A Young
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)
GSE94822 Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma [ChIP-Seq]
GSE94824 Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma
BioSample SAMN06324658
SRA SRX2555293

Supplementary file Size Download File type/resource
GSM2486159_20161217_5288.7816.rpm.WIG.gz 85.0 Mb (ftp)(http) WIG
GSM2486159_BE2C_ISL1_peaks.bed.gz 483.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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