|
| Status |
Public on Oct 12, 2017 |
| Title |
Control_108h (41-28) |
| Sample type |
SRA |
| |
|
| Source name |
Control_108h
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/cJ
tissue: mammary gland
reproductive status: OVX at 21d
agent: Control
time: 108h
|
| Treatment protocol |
After a 7d recovery period, mice were fed either a defined control diet (AIN 93G based) or the control diet with 2.7% fat as conjugated linoleic acid (CLA). Another group was fed the control diet and administered estrogen in the drinking water (200 nM). Mice were euthanized by CO2 inhalation 60, 84, 108, or 132h after starting treatment.
|
| Growth protocol |
Balb/cJ mice were ovariectomized at 21d of postnatal age.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The lymph node was removed from one #4 inguinal mammary gland and the tissue proximal to the teat and extending to the region where the lymph node was excised was flash frozen in liquid nitrogen. Tissues were stored at -80C until further processing. Total RNA was extracted using TriReagent (Qiazol) and DNase treated in solution followed by an on-column clean-up. RNA integrity was assesed using automated gel electrophoresis (Bio-Rad Experion). Samples with an RQI between 7.5-9.4 (mean 8.7) were submitted for library preparation.
Libraries were constructed by the UC Davis DNA Technologies Core using the Stranded mRNA-Seq Kit for Illumina platforms with poly-A enrichment with 10 cycles of PCR. All libraries were pooled and sequenced across 4 lanes. There were an average of 39 million reads per library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
CountEarly_use.txt
Early_RPKM_export_07_09_2016.txt
|
| Data processing |
Data were imported into the CLC Genomics Workbench. Demultiplexed libraries were concatenated to a single file for each sample ID.
Adapter sequences were trimmed from the reads using the CLC Genomics Workbench. Quality Control reports were created and inspected for each sample.
Reads were mapped to the mouse genome (Mus musculus GRCm38.84) using the CLC Genomics Workbench.
Matrix files with raw counts and RPKM for each gene were exported from the CLC Genomics Workbench.
Genome_build: Mus musculus GRCm38.84
Supplementary_files_format_and_content: tab delimited text files containing RPKM for each sample, and tab delimited text files containing raw counts.
|
| |
|
| Submission date |
Jan 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Grace E Berryhill |
| E-mail(s) |
geberryhill@ucdavis.edu
|
| Phone |
5307524970
|
| Organization name |
University of California, Davis
|
| Department |
Animal Science
|
| Lab |
Russell C Hovey Laboratory
|
| Street address |
One Shields Avenue
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE94121 |
The transcriptome of estrogen-independent mammary growth induced by dietary conjugated linoleic acid |
|
| Relations |
| BioSample |
SAMN06275198 |
| SRA |
SRX2521147 |
