|
| 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 |
| 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 |
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 |
|
| Relations |
| BioSample |
SAMN14972429 |
| SRA |
SRX8363486 |
