|
| Status |
Public on Jun 13, 2014 |
| Title |
CAL-1-E2-2-ChIP |
| Sample type |
SRA |
| |
|
| Source name |
CAL-1 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CAL-1
antibody: E2-2 Ab is a rabbit monoclonal Ab generated in Dr. Louis Staudt's lab
|
| Growth protocol |
Cells were maintained in RPMI 1640 with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fragmented from lysated using covaris protocol in a covaris sonicator, and Mtg16 or E2-2 -DNA complexes were isolated with antibody.
Library construction and sequencing were performed at the Yale Center for Genome Analysis. Briefly, magnetic AMPure XP beads (Beckman Coulter) are used to purify the user-sheared DNA samples and remain with the sample throughout library construction. Following each process step, DNA is selectively precipitated by weight and re-bound to the beads through the addition of a 20% polyethylene glycol, 2.5 M NaCl solution. Following fragmentation, T4 DNA polymerase and T4 polynucleotide kinase blunt end and phosphorylate the fragments. The large Klenow fragment then adds a single adenine residue to the 3' end of each fragment and custom adapters (IDT) are ligated using T4 DNA ligase. The inserts are size-selected in-solution and adapter-ligated DNA fragments are then PCR amplified using custom-made primers (IDT). During PCR, a unique 6 base index is inserted at one end of each DNA fragment. Samples were sequenced on a single-end version 3 Illumina flow cell on a HiSeq 2000
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
"subpeaks" bed file is generated by splitting the peaks in the peaks_peaks.bed file
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
ChIPSeq reads were aligned to the human hg19 genome using the short read aligner Bowtie (2.0.0)
Significantly enriched ChIP regions were identified using the Model-based analysis of ChIP-Seq (MACS) (1.4.0) using input chromatin as controls
Identified enriched regions were further split using PeakSplitter v1.0 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: BED files were generated by MACS. The 5th column of MACS-generated bed files is the -10*log10pvalue of peak region.
|
| |
|
| Submission date |
Jan 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hiyaa Singhee Ghosh |
| E-mail(s) |
hg2238@columbia.edu
|
| Organization name |
Columbia University Medical Center
|
| Street address |
701 W 168th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE43876 |
Mtg16 regulates E protein activity and lineage specification in dendritic cell development (ChIP-seq) |
| GSE43963 |
Mtg16 regulates E protein activity and lineage specification in dendritic cell development |
|
| Relations |
| SRA |
SRX220960 |
| BioSample |
SAMN01908573 |
