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Sample GSM4693022 Query DataSets for GSM4693022
Status Public on Oct 25, 2021
Title NGP_Ctrl_H3K27ac_MWZ5969 [Lab: Look]
Sample type SRA
 
Source name Neuroblastoma
Organism Homo sapiens
Characteristics cell type: NGP
chip antibody: H3K27Ac
antibody manu.: Abcam
antibody catalog: ab4729
antibody lot: GR3211959-1
young_id: 20180825_7513
drug: DMSO
treatment protocol: DMSO, 12 days
Growth protocol Cells were grown in 6-well plates in RPMI media containing 10% FBS and 1% pen-strep. Cells were treated with DMSO or ATRA (5uM) for 12 days.
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 23, 2020
Last update date Oct 25, 2021
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)
GSE154999 Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN (ChIP-Seq)
GSE155002 Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN
Relations
BioSample SAMN15634859
SRA SRX8814877

Supplementary file Size Download File type/resource
GSM4693022_20180825_7513.10054.rpm.WIG.gz 66.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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