|
| Status |
Public on Apr 16, 2012 |
| Title |
V9M_H3K4me3_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Colon cancer_H3K4me3_ChIPSeq
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Colon Cancer
chip antibody: H3K4me3
chip antibody vendor: Active Motif
chip antibody cat. #: 39159
chip antibody lot #: 016 09004
|
| Growth protocol |
Primary colon cancer cell lines were grown in 15 cm dishes to 70% confluency prior to harvest for ChIP-seq and RNA extraction. Normal colon crypts were isolated from surgical specimens of colon excised past the normal margin of tumors. Specimens were verified by microscopy to be free of any cancer cells. Samples were washed in cold PBS, placed in cold DMEM+10%FBS, and then transported from the operating room to the laboratory within 8 hours of surgery. Extraction of colonic crypts was performed by EDTA fractionation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 17 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
V9M
processed data file: all_mFOLD7_MACS_peaks_H3K4me3.txt
genome build: hg18
|
| Data processing |
MACS peak calls: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)[.txt processed files are available as Series Supplementary files]; paired end data files were treated as single end experiments.
|
| |
|
| Submission date |
Mar 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Scacheri |
| E-mail(s) |
pxs183@case.edu
|
| Phone |
216-368-3458
|
| Organization name |
Case Western Reserve University
|
| Street address |
10900 Euclid Ave; BRB 647
|
| City |
Cleveland Heights |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE36204 |
Epigenomic enhancer profiling defines a signature of colon cancer [ChIP-seq] |
| GSE36401 |
Epigenomic enhancer profiling defines a signature of colon cancer |
|
| Relations |
| SRA |
SRX124713 |
| BioSample |
SAMN00794461 |
