|
| Status |
Public on Nov 01, 2013 |
| Title |
300+100_a |
| Sample type |
SRA |
| |
|
| Source name |
cells in culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: CXCL12 (300ng/mL) + IGF1 (100ng/mL)
|
| Treatment protocol |
Cells were starved in 0.2% serum for 24hrs and treated with CXCL12 + IGF1 at two different concentrations for 6 hrs. Two biological replicates were included for each condition.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).
RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling was performed with Illumina Casava v1.8.1
Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0
Gene-level expression counts were determined with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
|
| |
|
| Submission date |
Jan 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Jin |
| E-mail(s) |
jinx@mskcc.org
|
| Phone |
6468882540
|
| Organization name |
Memorial Sloan-Kettering Cancer Center
|
| Department |
Cancer Biology and Genetics
|
| Street address |
417 East 68th Street
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE43296 |
Polysome-associated mRNA profiling of cancer cells in response to CXCL12 and IGF1 |
|
| Relations |
| SRA |
SRX215398 |
| BioSample |
SAMN01883071 |
