|
| Status |
Public on Sep 28, 2017 |
| Title |
Max_ChIP-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Merkel cell carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MKL-1
cell type: Merkel cell carcinoma
merkel cell polyomavirus: positive
chip antibody: Max (Santa Cruz, SC-197)
|
| Growth protocol |
MKL-1 cells grow as suspension clumps in RPMI medium supplemented with 10% FBS, Penicillin-Streptomycin, and glutamax
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei as described in 'ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. 2009 Methods 48, no. 3: 240-248.'
10 ng of DNA from ChIP experiments or input DNA were prepared for sequencing with NEBNext ChIP-seq Library Prep Reagent Set for Illumina (New England Biolabs). Diluted libraries were used for 50 cycles single-end sequencing on HiSeq2000 system (Illumina) at the Center for Cancer Computational Biology (CCCB) at Dana-Farber Cancer Institute following the manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Peaks also called using both replicates = MAX.peaks_bothreps.bed, MAX.peaks_bothreps.txt. These files are available on the series record.
|
| Data processing |
FASTQ data were mapped to human hg19 genome using Bowtie (bowtie-0.12.7)
Duplicate peaks were removed (macs2 filterdup function) and the reads were normalized (macs2 randsample) so that the input and the ChIP sample have the same number of reads using MACS2 (MACS-2.0.10.20130306).
Peaks were called using MACS2 with hs as the genome size (macs2 callpeak ).
Using BETA(1.0.5), the ChIP-seq peaks were incorporated with the differential expression data (diffexp.txt file from RNA-seq analysis) to find the direct targets and predict motifs. Parameters: BETA plus --peakfile STHA_1.peaks_peaks.bed --diff_expr diffexp.txt --kind O --genome hg19
genome build: hg19
processed data files format and content: bed files of called peaks and macs output
|
| |
|
| Submission date |
Jun 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jingwei Cheng |
| E-mail(s) |
jingweic@gmail.com
|
| Phone |
617-632-4797
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
James A. DeCaprio
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE69877 |
MCPyV ST, MAX and the TRRAP complex cooperate to bind to Transcription Start Sites |
| GSE69878 |
MCPyV ST activates Max target genes by recruiting TRRAP/EP400 complex |
|
| Relations |
| BioSample |
SAMN03775173 |
| SRA |
SRX1058475 |
