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Sample GSM1896284 Query DataSets for GSM1896284
Status Public on Nov 03, 2015
Title Het (Q111) 10 month Male Hippocampus mRNA rep2
Sample type SRA
 
Source name Het (Q111) 10 month_Male_Hippocampus
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Het (Q111) Knock-In
age: 10 months
Sex: Male
tissue: Brain - Hippocampus
tissue: Brain - Hippocampus
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description 372535_45431_1_L6.D702
Data processing Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omnisoft OSA 2.0
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 Sep 28, 2015
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)
GSE73503 Transcriptome profiling in knock-in mouse models of Huntington's disease [Hippocampus_mRNA]
GSE73508 Transcriptome profiling in knock-in mouse models of Huntington's disease [cerebellum; hippocampus]
Relations
SRA SRX1292521
BioSample SAMN04116291

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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