|
| Status |
Public on Oct 18, 2015 |
| Title |
Input for ChIP:Be2c_103014 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BE2C
system: Blood
chip antibody: None
antibody manu.: n/a
antibody catalog: n/a
|
| Treatment protocol |
No
|
| Growth protocol |
Kelly/SHSy5Y/BE2C was grown in RPMI with 10% FBS and 1% penn/strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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.
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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
young_id: 20141126_3342
|
| Data processing |
Sample(s) 20141126_3337, 20141126_3340, 20141126_3342 aligned to the hg19 reference genome using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Sample(s) 20141124_3330, 20141124_3332, 20141124_3333 aligned to the hg19 reference genome using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 46
Supplementary_files_format_and_content: WIG files represent counts of aligned reads in 50 bp bins with each read being extended 200 in the direction of alignment using MACS. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
Feb 05, 2015 |
| 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 |
GPL16791 |
| Series (1) |
| GSE65664 |
Genetic predisposition to neuroblastoma mediated by a single nucleotide polymorphism within a LMO1 oncogene super-enhancer element |
|
| Relations |
| BioSample |
SAMN03329763 |
| SRA |
SRX866616 |
