|
| Status |
Public on Apr 05, 2012 |
| Title |
P493-6_T24_H3K4ME3 |
| Sample type |
SRA |
| |
|
| Source name |
B-cell lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me3
antibody details (vendor, catalog number): Millipore 07-473
cell type: P493-6
|
| Treatment protocol |
Tetracycline repressed cMyc transgene expression. cMyc expression released for 24 hours.
|
| Growth protocol |
RPMI 1640 + FBS. Tetracycline repressed cMyc transgene expression. cMyc expression released for 24 hours.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell 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 |
| |
|
| Description |
Chromatin IP against H3K4me3 in P493-6 T=24 hours
barcode (already removed): GATCAG
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Supplementary_files_format_and_content: Alignment (ylf) files: The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>1 (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2 (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
etc..
|
| |
|
| Submission date |
Mar 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE36354 |
Transcriptional Amplification in Tumor Cells with Elevated c-Myc |
|
| Relations |
| SRA |
SRX129078 |
| BioSample |
SAMN00811111 |
