|
| Status |
Public on Sep 15, 2015 |
| Title |
V852 DACOR1 Lentivirus 1 |
| Sample type |
SRA |
| |
|
| Source name |
Patient-derived colon cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cancer type: Colorectal cancer
Sex: Male
cell line: V852
transduction: DACOR1 Lentivirus
|
| Treatment protocol |
V852 cells were transduced with lentiviral supernatant and treated with 1ug/ml puromycin to target cells that were not infected with lentivirus.
|
| Growth protocol |
Grown in MEM media with 2% FBS, 2.4 mM L-glutamine, 10 ug/ml insulin, 2 ug/ml human transferrin, 2 ug/ml selenium, 1 ug/ml hydrocortisone, 50 ug/ml gentamicin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy® Mini Kit (Qiagen) according to the manufacturer’s protocol. An added DNase (Qiagen) treatment step was included after the first wash.
Library preparation as per Scriptseq Complete Gold (Human/Mouse/Rat) from Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The 100 bp paired-end strand-specific sequencing reads were mapped to hg19 using TopHat with 2 mismatches allowed for full-length reads.
The raw reads were mapped to human gene annotated in RefSeq database using Cufflinks V2.0.2 and expression valued were calculated at fragment per kilobase of exon per million of mapped fragments (fpkm)
CuffDiff was used to for identifying differentially expressed genes. P-value of < 0.05 and q-value of < 0.05 were used as cut-offs for identification of differential expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delinated text file are provided with RefSeq gene ID along with the normalized fpkm value for each sample.
|
| |
|
| Submission date |
Aug 19, 2015 |
| 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 |
GPL16791 |
| Series (1) |
| GSE58989 |
DNMT1-associated long non-coding RNA regulate global gene expression and DNA methylation in colon cancer |
|
| Relations |
| BioSample |
SAMN04001580 |
| SRA |
SRX1158931 |
