|
| Status |
Public on Feb 14, 2018 |
| Title |
shGFP input DNA |
| Sample type |
SRA |
| |
|
| Source name |
A375 melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: A375 melanoma cells
antibody: none
stable knockdown: EGFP control
|
| Treatment protocol |
Stable knockdown of GDF6 or EGFP control
|
| Growth protocol |
A375 cells grown in 10cm tissue culture plates passaged on reaching 70-90% confluency
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using the Simple ChIP Plus Enzymatic Chromatin IP kit as per manufacturer’s instructions (Cell Signaling#9001) with the phospho-SMAD1/5/8 antibody (Cell Signaling#11971; 1:100).
ChIP-ed DNA fragments were added with 'A' base to the 3' end and adapters were ligated. This was followed by PCR amplfication and size selection (100-300bp). After QC, these were used for cluster preparation and HiSeq sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the human GRCh37 genome assembly using Bowtie version 1.0.0
PCR duplicates were filtered out from the aligned reads
Peaks were called using MACS2 (v 2.1.1.20160226) with default q-value.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: tab-delimited files were generated using MACS2. Information include: chromosome name; start position of peak; end position of peak; length of peak region; absolute peak summit position pileup height at peak summit, -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10); fold enrichment for this peak summit against random Poisson distribution with local lambda, -log10(qvalue) at peak summit
|
| |
|
| Submission date |
Jun 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dr Yvonne Edwards, PhD |
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Bioinformatics Core
|
| Street address |
373 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE83347 |
Differential gene expression of human melanoma cells [ChIP-seq] |
| GSE83400 |
GDF6-induced BMP signaling reawakens a neural crest identity in melanoma to prevent cell death and differentiation |
|
| Relations |
| BioSample |
SAMN05250004 |
| SRA |
SRX1845647 |
