|
| Status |
Public on Jul 21, 2013 |
| Title |
MCF7_10-uM-CHX_IGG |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: breast cancer cell line
cell line: MCF7 cells
antibody: IGG (Santa Cruz, sc-2027, Lot# C2210)
treatment: Cycloheximide (10 µM)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline. ChIP-Seq reads were aligned to HG18 using ELAND software (Illumina).
Identification of enriched genomic regions was performed as described previously (Guenther et al., 2008). Briefly, each ChIP-Seq read (a maximum of two repeat reads were allowed) was extended 100 bp to approximate the middle of the sequenced fragment. The extended fragments were subsequently allocated to 25 bp bins across the genome. Read density for each bin was calculated and enriched bins were identified by comparison to a Poisson background model using a p-value threshold of 10-12. The minimum ChIP-seq read density required to meet this threshold for each dataset is indicated in Table S1. Enriched bins within 200 bp were combined to form enriched regions. Enriched regions less than 100 bp were removed. Because of the non-random nature of background reads, enriched bins and regions were also required to have an eight-fold greater ChIP-seq density versus a nonspecific control IgG immunoprecipitation performed under identical conditions. All RefSeq genes that were within 8 kb of enriched regions were considered to be enriched genes. Enriched genes and regions for all experiments are listed in Table S1.
Genome_build: HG18
Supplementary_files_format_and_content: Processed data is provided as .xls. It contains the genes that are located within 8 Kb of each region (enriched genes) for each cell line and condition.
|
| |
|
| Submission date |
Apr 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Marc Mendillo |
| Organization name |
Whitehead Institute for Biomedical Research
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE45852 |
Tight coordination of protein translation and heat shock factor 1 activation supports the anabolic malignant state [ChIP-Seq] |
| GSE45853 |
Tight coordination of protein translation and heat shock factor 1 activation supports the anabolic malignant state |
|
| Relations |
| SRA |
SRX262142 |
| BioSample |
SAMN02009218 |
