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Sample GSM2718426 Query DataSets for GSM2718426
Status Public on Feb 12, 2019
Title Control 2
Sample type SRA
Source name Ovary
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 15 weeks
tissue: Ovary
diet: standard chow
sample group: control
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 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 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
BioSample SAMN07416876
SRA SRX3038571

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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