|
Status |
Public on Nov 15, 2017 |
Title |
TEAD4 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: anti-TEAD4 (ab58310; abcam)
|
Treatment protocol |
primary antibody was ab58310; abcam
|
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 |
SAMN05390593 |
SRA |
SRX1948680 |