|
| Status |
Public on Nov 01, 2013 |
| Title |
M6 |
| Sample type |
SRA |
| |
|
| Source name |
mammary tumor xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: EGFP-10a+ MDA-MB-231
protocol: supplemented with 1:1 ratio of MSC
|
| Growth protocol |
EGFP-L10a+ MDA-MB-231 cancer cells were orthotopically injected into the mammary fat pad with or without 1:1 ratio of human bone marrow derived mesenchymal stem cells (MSCs). The mammary tumors were retrieved for TRAP-RNAseq profiling after 3 weeks. Five biological replicates from different mice were included in the "with MSC" group (M), and four biological replicates from different mice were included in the "without MSC" group (A).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed 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 |
| |
|
| Description |
supplemented with 1:1 ratio of MSC
|
| 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 06, 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) |
| GSE43306 |
Translating transcriptome of cancer cells in situ in mesenchymal-rich tumor microenvironment |
|
| Relations |
| SRA |
SRX215401 |
| BioSample |
SAMN01883074 |
