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Sample GSM2036980 Query DataSets for GSM2036980
Status Public on Jan 11, 2016
Title Het (Q111) 6 months Male White Adipose (Gonad) miRNA rep2
Sample type SRA
 
Source name White Adipose tissue around Gonad
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: White Adipose tissue around Gonad
genotype: Het (Q111) Knock-In
age: 6 months
Sex: Male
housing condition: housed with Het (Q111) mice
Extracted molecule total RNA
Extraction protocol Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description 403467_24244.1_LB30
Data processing Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omnisoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omnisoft: Trimming /Mode=TrimByQuality /ReadTrimQuality=2; Options /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse B.38, gene models version Ensembl R.75
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample
 
Submission date Jan 11, 2016
Last update date May 15, 2019
Contact name Jeff Aaronson
E-mail(s) jeff.aaronson@chdifoundation.org
Phone (609) 945-9616
Organization name CHDI
Department Discovery & Systems Biology
Street address 155 Village Boulevard, Suite 200
City Princeton
State/province New Jersey
ZIP/Postal code 08540
Country USA
 
Platform ID GPL13112
Series (2)
GSE76738 Transcriptome profiling in knock-in mouse models of Huntington's disease. [gonadal adipose miRNA]
GSE76753 Transcriptome profiling in knock-in mouse models of Huntington's disease [gonadal adipose mRNA and miRNA]
Relations
BioSample SAMN04396585
SRA SRX1528008

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

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