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Sample GSM2470085 Query DataSets for GSM2470085
Status Public on Oct 12, 2017
Title Control_60h (41-78)
Sample type SRA
 
Source name Control_60h
Organism Mus musculus
Characteristics strain: Balb/cJ
tissue: mammary gland
reproductive status: OVX at 21d
agent: Control
time: 60h
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 SAMN06275189
SRA SRX2521156

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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