|
Status |
Public on Nov 01, 2013 |
Title |
0+0_b |
Sample type |
SRA |
|
|
Source name |
cells in culture
|
Organism |
Homo sapiens |
Characteristics |
cell line: MDA-MB-231 treatment: CXCL12 (0ng/mL) + IGF1 (0ng/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 |
SRX215395 |
BioSample |
SAMN01883068 |