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Sample GSM1605173 Query DataSets for GSM1605173
Status Public on Feb 15, 2016
Title WT 10 month Male cortex mRNA rep2
Sample type SRA
 
Source name cortex
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: cortex
genotype: Wild Type
age: 10 month
Sex: Male
housing condition: housed with Het (Q20) mice
Extracted molecule polyA 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 300187_Q20B0009_01_L7.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000
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:
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: Text file containing abundance measurements in FPKM
Supplementary_files_format_and_content: Text file containing abundance measurements in counts
 
Submission date Feb 09, 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)
GSE65770 Transcriptome profiling in knock-in mouse models of Huntington's disease [Cortex_mRNA]
GSE65776 Transcriptome profiling in knock-in mouse models of Huntington's disease [striatum; cortex; liver; tissue survey]
Relations
BioSample SAMN03334511
SRA SRX869816

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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