|
| Status |
Public on May 13, 2015 |
| Title |
Inputs pool |
| Sample type |
SRA |
| |
|
| Source name |
colon cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1
cell type: colon cancer cells input
antibody: none, input
|
| Treatment protocol |
For transduction of DLD1 cells, lentiviruses at a multiplicity of infection of 10-60 were added to the culture medium in the presence of 8 g/ml polybrene (Sigma) for 8 h, typically yielding more than 95% transduced (GFP-positive) cells.
|
| Growth protocol |
All cell lines used in this study were maintained in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum and 2 mM L-glutamine (Invitrogen, Paisley, UK).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP samples were processed into sequencing libraries with a ChIP-Seq sample preparation kit (Illumina) in accordance with the manufacturerâs instructions 2. Briefly, each sample was electrophoresed on agarose gel and a fraction of 100-200 bp was taken. Extracted DNA was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "ChIP Sequencing Sample Prep Guide" (part # 11257047 Rev. A), with the exception that gel extraction was replaced with Agencourt AMPure XP (BeckmanCoulter) bead purification. Each adapter-ligated library was PCR amplified with Illumina PE primers for 15 cycles. Independent aliquots were done with Phusion High-Fidelity DNA pol (Finnzymes Reagents) and Accuprime GC Rich pol (Invitrogen), and pooled after amplification. The resulting purified DNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on the Genome Analyzer IIx (GAIIx; Illumina) by following manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
input DNA
|
| Data processing |
Alignment: Unfiltered 40 bp sequence reads were aligned against the human reference genome (hg18 (NCBI build 36.1, March 2006) using Illumina's ELANDv2 algorithm on its "eland_extended" mode from within CASAVA-1.7 package. Raw sequences were defined as reads passing purity filter before genome alignment. Only the reads with a unique alignment in the reference genome were used for the peak detection.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
|
| |
|
| Submission date |
Aug 03, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Agustin F Fernandez |
| E-mail(s) |
affernandez@hca.es, agusff@gmail.com
|
| Phone |
985652411
|
| Organization name |
Oviedo University-HUCA
|
| Department |
IUOPA
|
| Lab |
Epigenetics
|
| Street address |
Avenida de Roma s/n
|
| City |
Oviedo |
| State/province |
Asturias |
| ZIP/Postal code |
33011 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE31170 |
Nuclear DICKKOPF-1 as a biomarker of chemoresistance and poor clinical outcome in colorectal cancer |
|
| Relations |
| SRA |
SRX088973 |
| BioSample |
SAMN00691497 |
