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Sample GSM3959460 Query DataSets for GSM3959460
Status Public on Jul 20, 2020
Title NGP_ARID1A_mut#1_input
Sample type SRA
 
Source name Neuroblastoma
Organism Homo sapiens
Characteristics cell line: NGP
cell type: ARID1A-/- #1
chip antiboy: None
Growth protocol The NGP neuroblastoma cell line was maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO),and 0.5ug/ml puromycin (Sigma #P8833).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.2.9 with configuration -p 8 -x $SHARED_DATABASES/bowtie2_indexes/hg19 -U
Data were filtered using SAMtools version 1.3.1 with configuration samtools view -bS -q 20
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files represent counts of aligned reads within 20 bp bins with each read being extended 75 in the direction of alignment. Counts are in reads-per-million.
 
Submission date Jul 22, 2019
Last update date Jul 20, 2020
Contact name Ting Tao
E-mail(s) taot@zju.edu.cn
Organization name Children's Hospital, Zhejiang University School of Medicine
Lab Ting Tao
Street address 3333 Binsheng Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310052
Country China
 
Platform ID GPL18573
Series (2)
GSE134626 ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression [ChIP-seq]
GSE134632 ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression
Relations
BioSample SAMN12334612
SRA SRX6483136

Supplementary file Size Download File type/resource
GSM3959460_Mu1_input_DNA.CPM.bw 144.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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