|
| Status |
Public on Sep 02, 2015 |
| Title |
8pDOX_chip_h3k27me3 |
| Sample type |
SRA |
| |
|
| Source name |
fibroscarcoma cell line HT1080
|
| Organism |
Homo sapiens |
| Characteristics |
dox treatment: 5day DOX
antibody: H3K27me3 (Active Motif 61017)
integration: chr8
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was done as previous (Hawkins et al.,Cell stem cell 2010, 6(5):479-491) , using 20ug of chromatin and 3ug of antibody was used per IP
ChIP library was prepared according to Illumina protocol with modifications according to Hawkins et al.,Cell stem cell 2010, 6(5):479-491.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Single-end 36bp reads
|
| Data processing |
Fastq reads from RNA-seq were mapped to hg18 using Tophat with UCSC hg18 gene annotations, outputting only uniquely mapped reads.
FPKM values were obtained through Cufflinks.
Fastq reads from ChIP-seq were mapped to hg18 using Bowtie, keeping only uniquely mapped reads. PCR-duplicates were excluded.
ChIP-seq bam files were analyzed using SeqMonk to obtain normalized levels of H3K27ac and H3K27me3. Read Count Quantitation was done using All Reads and correcting for total count per million reads. Sites pertaining to the higest and lowest 5% in the input samples were excluded in the analysis.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene in each RNA-seq samples; and RPM values for H3K27ac and H3K27me3 levels in 1Mb windows for each ChIP-seq samples.
|
| |
|
| Submission date |
Apr 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Carolyn Brown |
| E-mail(s) |
carolyn.brown@ubc.ca
|
| Phone |
604-822-0908
|
| Organization name |
University of British Columbia
|
| Department |
Medical Genetics
|
| Lab |
Brown Lab
|
| Street address |
2350 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE68109 |
Impact of flanking chromosomal sequences on localization and silencing by the ncRNA XIST |
|
| Relations |
| BioSample |
SAMN03496117 |
| SRA |
SRX1002802 |
