GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1895180 Query DataSets for GSM1895180
Status Public on Nov 03, 2015
Title Het (Q111) 10 month Female Cerebellum mRNA rep2
Sample type SRA
Source name Het (Q111) 10 month_female_cerebellum
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Het (Q111) Knock-In
age: 10 months
Sex: Female
tissue: Brain - Cerebellum
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 1.25 ug of total RNA were used to collect polyA-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 372507_45531_1_L1.D707
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 25, 2015
Last update date May 15, 2019
Contact name Jeff Aaronson
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)
GSE73468 Transcriptome profiling in knock-in mouse models of Huntington's disease [cerebellum_mRNA]
GSE73508 Transcriptome profiling in knock-in mouse models of Huntington's disease [cerebellum; hippocampus]
BioSample SAMN04114240
SRA SRX1288336

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap