|
| Status |
Public on Jun 23, 2020 |
| Title |
Untreated M/D tumor Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
mammary gland tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
agent: none
|
| Treatment protocol |
0.5 % NAM was added to the drinking water for 10 days. Drinking water was changed once a week
|
| Growth protocol |
M/D: Fifty mg slow-release (90 days) medroxyprogesterone acetate (MPA) pellets (Innovative Research of America) were implanted subcutaneously by surgery into 6-9 week-old female (day 0). Mice were administered 200 µL of a 5 mg mL-1 7,12-dimethylbenz[a]anthracene (DMBA; from Sigma-Aldrich) solution in corn oil (Sigma-Aldrich), by oral gavage once a week on weeks 1, 2, 3, 5, 6 and 7 after implantation of the MPA pellet. When tumors reached 0.25cm2 the animals were randomized to the different treatment groups.
AT3: For tumorigenicity assays, 1.0 x 10^6 AT3 cells were injected subcutaneously. When tumors reached 0.25cm2 the animals were randomized to the different treatment groups.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumors were removed from the mice and RNA freshly extracted using Qiagen RNeasy kits.
mRNA libraries were prepared using the Truseq mRNA library prep kit (Illumina) and sequenced in paired end mode (2X75)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
C6A-Exp1_S2
|
| Data processing |
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Mouse FAST DB v2016_1 were also provide
|
| |
|
| Submission date |
May 21, 2020 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Pierre de la Grange |
| E-mail(s) |
pierre.delagrange@genosplice.com
|
| Organization name |
GenoSplice technology
|
| Department |
Paris Biotech Santé
|
| Street address |
29, rue du Faubourg Saint-Jacques
|
| City |
Paris |
| ZIP/Postal code |
75014 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE150967 |
Mammary gland tumor immunoinfiltrate analysis |
| GSE150968 |
Immunoinfiltrate analysis |
|
| Relations |
| BioSample |
SAMN14987731 |
| SRA |
SRX8374112 |
