|
| Status |
Public on Nov 15, 2017 |
| Title |
Input ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow metastatic neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neuroblastoma cell line
cell line: SK-N-BE2
chip antibody: input
|
| Treatment protocol |
input antibody
|
| Growth protocol |
neuroblastoma cell lines were sourced from the American Type Tissue Culture Collection, and kept in growth medium of RPMI+10% heat-inactivated FCS with 1% penicillin–streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed for protein, with subsequent protein quantified by spectrophotometry. Protein was resolved on 8–14% Tris-Bis gels, transferred to PVDF membranes, blocked and subjected to primary and secondary antibodies
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The RNA-Seq libraries were aligned to hg19 human genome using TopHat
Raw counts of each gene were generated using GenomicFeatures R-system package (Bioconductor)
The data was then normalized using voom implemented in edgeR R Bioconductor package
The ChIP-Seq libraries were aligned to hg19 human genome using bowtie 1.1.1 with parameters -k 2 -m 2 --best --sam and -l 40
Peaks were called using MACS2 with corresponding input or IgG control, -p 1e-9 and --keep-dup=auto
Genome_build: hg19
Supplementary_files_format_and_content: txt and bed files were generated containing gene level normalized values and peak calling respectively
|
| |
|
| Submission date |
Jul 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gonzalo Lopez |
| Organization name |
Mount Sinai School of Medicine
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
1399 Park avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE84389 |
Network-based, cross-cohort discovery of transcriptional mechanisms presiding over maintenance of high-risk neuroblastoma subtype state |
|
| Relations |
| BioSample |
SAMN05390594 |
| SRA |
SRX1948681 |
