|
| Status |
Public on Aug 12, 2015 |
| Title |
Mouse3L_MCF7-EGFP |
| Sample type |
SRA |
| |
|
| Source name |
Stroma and tumor of MCF7-EGFP cells injected into left cleared 4th inguinal mammary fat pad, mouse 3
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
mouse strain: Nude Foxn1nu
tissue: MCF7-EGFP tumor and mouse mammary tissue
|
| Treatment protocol |
cells mixed with BD Matrigel Basement Membrane Matrix (BD Biosciences, cat. no. 356234) and injected into the left and right cleared 4th inguinal mammary fat pads; tumors were allowed to grow for 8 weeks (average tumor volume of 500mm3), supplemented with estrogen and progesterone pellets (Innovative Research of America) to support growth.
|
| Growth protocol |
cells maintained in DMEM, high glucose, pyruvate (Gibco, cat. no. 41966-029) supplemented with 10% fetal bovine serum (Gibco, cat. no. 10270-106) and 1% penicillin-streptomycin (10,000 U/mL, Gibco, cat. no. 15140-122) at 37°C in a humidified 5% CO2 atmosphere
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
We used the “Lysis and Homogenization: 10-100mg Frozen or Fresh Fibrous Tissue, Mortar and Pestle Protocol” of the PureLink RNA Mini Kit (Ambion, cat. no. 12183-018A)
We used the kit TruSeq RNA Sample Prep Kit v2–48, Set B (Illumina®, cat. no. RS-122-2002)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned using STAR to genomes mm10 and hg19
Reads were separated for different species using S^3 (https://github.com/danielramskold/S3_species-specific_sequencing) with default settings (-Ms 1 -Mu 1 -D 2)
Unique reads were selected using mapping quality threshold 255
Gene expression values were calculated using rpkmforgenes.py (http://sandberg.cmb.ki.se/rnaseq) with options -rmnameoverlap -bothendsceil and using RefSeq annotation from 1 July 2014
MicroRNAs and snoRNAs were removed
RPKM values were TMM normalized
Supplementary_files_format_and_content: RPKM expression values and read counts (tab-delimited text format)
|
| |
|
| Submission date |
Mar 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Ramsköld |
| E-mail(s) |
daniel.ramskold@ki.se
|
| Organization name |
Karolinska Institutet
|
| Lab |
Rickard Sandberg's group (rickard.sandberg@ki.se) (2008-2014, 2018-); Rheumatology unit (2014-2018)
|
| Street address |
Nobels väg 3
|
| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL16512 |
| Series (1) |
| GSE66744 |
Decoding breast cancer tissue-stroma interactions using species-specific sequencing |
|
| Relations |
| BioSample |
SAMN03397489 |
| SRA |
SRX950742 |
