|
| Status |
Public on May 28, 2014 |
| Title |
siCIP2A |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231 breast cancer cell line
treatment: CIP2A siRNA
|
| Treatment protocol |
SET or CIP2A were knocked out by siRNA for 48hours. For OP449 treatment, cells were treated for 12 hours with 1μMOP449.
|
| Growth protocol |
IMDM+5%FBS+1XPen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells by Trozol reagent.
Total RNA was purified and reverse transcribed with oligo dT. Second strand DNA was synthesized and ligated to proprietary indexed adapters. Ligated material was amplified using Illumina genomic primers and sequenced on an Illumina GAII sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Samples were sequenced on an Illumina HiSeq 2000 and assembled into fastq files using the CASAVA software at the OHSU Massively Parallel Sequencing Shared Resource.
Sequences were aligned to the human hg19 genome using Bowtie version 1.0.0 and seting requiring unique alignments with no more than 3 mismatches.
Trim settings for Bowtie were selected to discard the first 4 bases, align to the next 44, and discard remaining bases from each sequence.
Aligned sequences that fell in exonic regions of RefSeq gene models were counted and normalized for sequencing depth.
Genes that showed low normalized sequence counts for all samples were discarded from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited .txt file containing normalized sequence counts for gene models before filtering out low expression genes.
|
| |
|
| Submission date |
May 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Rosalie Sears |
| E-mail(s) |
searsr@ohsu.edu
|
| Phone |
5034946885
|
| Organization name |
OHSU
|
| Department |
MMG
|
| Street address |
3181 S.W. Sam Jackson Park Rd
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239-3098 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE58008 |
Targeting c-MYC by antagonizing PP2A inhibitors in breast cancer |
|
| Relations |
| BioSample |
SAMN02800676 |
| SRA |
SRX554354 |
