|
| Status |
Public on Feb 12, 2019 |
| Title |
HFLN 3 |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: 15 weeks
tissue: Ovary
diet: 60% HFD
sample group: lean after HFD
|
| Treatment protocol |
HFLN and HFOB mice were fed a 60% fat diet for 10 weeks, control were fed a 16% fat standard chow.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ovaries were removed and flash frozen in liquid nitrogen, RNA was extracted with Qiagens Rneasy mini kit (#74104) following manufacture protocols.
Libraries were prepared with Illumina TruSEQ mRNA stranded library construction kit. Barcode sequences are as follows, sample 1 - ACAGTG, sample 2 - GCCAAT, sample 3 - CTTGTA, sample 4 - GTGAAA, sample 5 - CGATGT, sample 6 - TGACCA, sample 7 - CAGATC, sample 8 - CCGTCC, sample 9 - ATGTCA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Cuffdiff_gene_FPKM_tracking.tabular
|
| Data processing |
Base calling was conducted using the asecalling software RTA version 2.7.3
Adaptor trimming and trimming based on read quality (sliding window function with a quality cutoff of 20 and minimum length of 50 bp) was performed with Trimmomatic (Galaxy version 0.32.3).
Sample reads were aligned to the mm10 reference genome with TopHat (Galaxy version 2.1.0)
Cufflinks (Galaxy version 2.2.1.0) was used to assemble transcripts and Cuffmerge (Galaxy version 0.0.6) was used to merge transcripts into a final transcript assembly.
Cuffdiff (Galaxy version 2.2.1.3) was used to assess differentially expressed genes between the groups.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files with the FPKM values for each group.
|
| |
|
| Submission date |
Jul 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Malgorzata Skaznik-Wikiel |
| Organization name |
University of Colorado School of Medicine
|
| Department |
Obstetrics and Gynecology
|
| Street address |
12700 East 19th Avenue
|
| City |
Aurora |
| State/province |
Colorado |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE101906 |
High-fat diet exposure, regardless of the induction of obesity, is associated with altered expression of genes critical for normal ovarian function |
|
| Relations |
| BioSample |
SAMN07416872 |
| SRA |
SRX3038575 |
