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Sample GSM4559740 Query DataSets for GSM4559740
Status Public on Jul 20, 2020
Title NGP_ctrl_input_for_ARID1A
Sample type SRA
Source name Neuroblastoma
Organism Homo sapiens
Characteristics cell line: NGP
genotype: control
chip antiboy: None
Treatment protocol 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 NovaSeq 6000
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. For ARID1A and its corresponding input ChIP-Seq, configuration -p 8 -x $SHARED_DATABASES/bowtie2_indexes/hg19 was used.
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 (50 for ARID1A and its corresponding input ChIP-Seq) in the direction of alignment. Counts are in reads-per-million.
Submission date May 19, 2020
Last update date Jul 20, 2020
Contact name Ting Tao
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 GPL24676
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
BioSample SAMN14972429
SRA SRX8363486

Supplementary file Size Download File type/resource 398.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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