|
| Status |
Public on Sep 15, 2015 |
| Title |
Gp2 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
cell line: HCT116
|
| Treatment protocol |
Cells were crosslinked with 0.3% formaldehyde for 10 minutes to preserve RNA-protein interactions
|
| Growth protocol |
The colon cancer cell line HCT116 was maintained in DMEM supplemented with 10% FBS and 1% antibiotics in 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclear lysates were incubated with an anti-flag antibody overnight to IP flag-DNMT1, and the entire complex was isolated using magnatic beads. The crosslinking was reversed and RNA was isolated via trizol
RNA-seq libraries were constructed using ScriptSeq V2 (Illumina) kit as recommended by the manufacturer
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Base calling was performed on instrument using real time analysis (RTA) followed by demultiplexing using CASAVA version 1.81
Reads were aligned to hg19 using TopHat version 2.0.11 with bowtie2 version 2.1.0 specifying library strategy as first-strand
Transcript abundance (reported as FPKM) was generated using cufflinks version 2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: Text-tab delimited file with FPKM for each Sample
|
| |
|
| Submission date |
Jul 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ahmad M Khalil |
| E-mail(s) |
amk175@case.edu
|
| Organization name |
Case Western Reserve University
|
| Department |
Genetics and Genome Sciences
|
| Lab |
BRB719
|
| Street address |
2109 Adelbert Rd
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE58989 |
DNMT1-associated long non-coding RNA regulate global gene expression and DNA methylation in colon cancer |
|
| Relations |
| BioSample |
SAMN02899067 |
| SRA |
SRX643097 |
