|
| Status |
Public on Feb 28, 2015 |
| Title |
Precursor Control |
| Sample type |
SRA |
| |
|
| Source name |
HT29 colon cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
sirna treated: High mIR23b Control
passages: Passages 12 -13
cell line: HT29
cell type: colon cancer
|
| Treatment protocol |
Cells were transfected with 50nm of MiR23b Prec, Antimir and their respective controls using Lipofectamine 2000 as a transfection reagent. Media was changed 24 hours post tranfection.
|
| Growth protocol |
HT29 cells were plated on 100 mm dish using McCoy medium (containing 5% FBS and 1% Pennicllin/Streptomycin) to reach a confluency of 90% at the day of transfection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated 48 hours post transfection using Trizol method.
RNA libraries were prepared using the standard Illumina protocols. HSA672 tag ATCACG. HSA673 tag CGATGT. HSA674 tag TTAGGC. HSA674 tag TGACCA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
base calling was done using bcl2fastq_1.8.3
Sequenced reads were trimmed for adapter sequence and mapped to hg19 whole genome using Tophat v2.0.11, with 1 mismatch, gtf file gencode.v11.annotation.gtf, --no-novel-juncs
Transcript abundance (fpkm) was calculated using Cufflinks V2.2.0 using compatible hits normalization and compared using the cuffdiff program
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff output diff file
|
| |
|
| Submission date |
Jul 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bruce Boman |
| E-mail(s) |
brucemboman@gmail.com
|
| Phone |
3186072764
|
| Organization name |
Helen F Graham Cancer Center and Research Institute
|
| Department |
CTCR
|
| Lab |
suite 4300
|
| Street address |
4701, ogletown-stanton road
|
| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE59290 |
MiRNA23B REGULATES SELF-RENEWAL AND CHEMORESISTANCE PROPERTIES OF COLON CANCER STEM CELLS |
|
| Relations |
| BioSample |
SAMN02906869 |
| SRA |
SRX648902 |
